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In our group, we are working in the field of small molecules interacting with proteins in order to affect their function. The first step of this work requires using software applications as docking algorithms, and it is essential the JChem package to create a canonical Smiles representation for our molecules to obtain a good 3D representation. On the other hand, we have developed a new method to estimate molecular properties, directly from the molecular smiles code (Article in press), therefore we need a canonical Smiles representation. LogS and LogP can be estimated quickly using this method, where 10.000 molecules can be computed per second.

Management of virtual libraries; development of new molecular descriptors; QSAR

We are interested in drug design and pharmacophore and structure based screening of new agonists of peroxisome proliferator activated receptors.

Organic Chemistry Laboratory Course of Cheminformatics Input of structures, database maintenance, extraction of chemical information

We teach students the International Baccalaureate Diploma programme for Chemistry. Personally I am keen to give as much exposure to computational methods and software as possible for pre-university students.

Try to use the software to analysize our small molecule 3D database to see their similarity and/or diversity.

We will be using this package to teach cheminformatics and drug discovery classes to our ug and pg students. we will also be using this package for our pg students project works (for research)

The CERMN (director : Pr S. Rault) is specialized in the design, synthesis and development of new potential drugs. These scientific activities concentrate mainly, these last years, in neurosciences and cancerology. The centre is composed by 12 professors and associated professors. From 1998 to 2003, the CERMN staff are the authors of 100 international publications and 12 international patterns. Personally, I am in charge of the molecular modelling department which has , as main activities, the ligand design on a structural basis. This research is in straight relation with the medicinal chemistry and pharmacology departments. Since a few years, we developed a software package for molecular modelling coupled to chemical databases and particularly our own chemical database (more than 6000 compounds). This experience in this field enabled us to be one of the main teams which worked actually at the installation of the new national chemical database (GDS/CNRS) intended to provide original chemical compounds for investigating new therapeutics. In molecular modelling, in the last years, we demonstrated that molecular design based on 3D pharmacophores could be carried out to obtain new ligands with an unique or a multiple controlled affinity. This hypothesis was studied initially on serotonin receptors and we obtained original ligands for 5-HT4, 5HT7 and 5-HT transporter . Since one year, we have started studies on several kinases.

Software will be used in our 20 seat Silicon Graphics Classroom. Course taught in this room are designed for both undergraduate and graduate students. Also used by structural and computational research groups at the University.

Student Research for molecular and biochemical learning

Use in lecture presentations.

Synthesis of medicinal compounds

to show student 3d models via a interactive whiteboard

Teaching: Software will be used in CH448/748, Computer-Aided Drug Design, for property calculations and construction of demo databases; Other activities as I learn more about the package. Research: Property calculations, integration with databases, and use in conjunction with tools we have developed (e.g. Shape Signatures, J. Med. Chem. 2003, 46, 5674-5690).

I’m a biochemistry professor at the Medical School at Oporto, Portugal, and would like to evaluate your programme to offer to my collegues (I’m resposable for the informatics in your lab) and eventually propose to the student.

Software is to be implemented for computational/physical chemistry courses.

I am in the Department of Bioinformatics at Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) in St. Augustin (close to Bonn, the former capital of Germany). Fraunhofer is a governmental “not for profit” research organisation in Germany. Fraunhofer Institutes exist in Germany, in other parts of Europe, in China and in the USA. Typically, Fraunhofer Institutes do applied research (I believe similar to the RAND corporation or the MITRE Institutes in the USA). The Department of Bioinformatics at Fraunhofer SCAI is involved in teaching at the “Bonn-Aachen Academy for Information Technology” (B-IT, please visit http://www.b-it-center.de/ for more information) in the “Life Science Informatics” curriculum and we have a history in virtual screening (molecular docking and similarity based screening). We want to use the JChem Modules for teaching purposes, demonstrating to students different approaches in the field of virtual screening and chemical databases. We want to offer a lecture “Applied Chemoinformatics” for the next winter term (2004) at B-IT and the accompanying practical course will introduce students to tools for molecular docking, similarity – based screening and chemical databases.

The application and development of computational techniques, NMR spectroscopy, and crystallography to structural problems in chemistry. Methods applied: semiempirical (AM1, PM3), HF, MP2, CCSD(T), QCISD(T), DFT and MM.

molecular and structural biology, protein folding

Abstract. Using concepts from federated databases, we propose a new methodology for the integration of heterogeneous bio-databases in the area of drug discovery. This methodology facilitates and accelerates the automatic integration of di erent data-types and formats, with an im- proved design for data management and standardization. Illustration of the methodology application is presented through the integration of two chemoinformatics databases.

We are interesting about virtual screening. Now we want to investigate the different methodics of QSAR and compare results with those obtained by docking.

Teaching chemistry and Biochemistry to undergraduates in Biology, Medicine and Biomedical Sciences

The general research focus of our lab is protein structure, dynamics, folding, and function relationships. The predominant technique of the lab is NMR. My work involves structural interactions that affect the function of neuropeptides. Some of this work is also used for teaching in the NMR course. The software will mostly be used for generating figures for presentations, however it may be used to generate figures for publication. Thanks!

I wish to explore the use of these tools in guiding directed evolution experiments. In the latter, we hope to modify the structure of AOAH, an enzyme that detoxifies LPS, in order to make it more soluble and expressible in E. coli. The ultimate goal is crystallize the enzyme for structural studies.

I am currently teaching an Introductory graduate course in Protein and Chemical Informatics. I and my students wish to use your software to provide a hands-on overview of some topics such as structure representation, chemical databases, similarity searching, property prediction, descriptors and docking. I also intend to use this for my research in understanding protein-ligand interactions.

pKa calculations on active sites of proteins.

Producing chemical structures for research presentations

ChemAxon product will be used for academic research in drug design. Modeling Protein interaction with small ligands. Calculating small molecules properties, 2D to 3D and 3D back to 2D conversions of small molecules. It is planned that ChemAxon product will be integrated as part of a larger assembly of programs aimed at serving Drug Design solution on the Internet for academic usage only!. This is however not yet implemented.

Analysis of Chemical compounds and their Biological Interactions

To teach applied chemistry to Medical School Students

Teaching: We are developing a web-based computional chemistry lab class which will be delivered to our Year 2, 3 and 4 Bachelors and Masters students. In this course we are trying to integrate all aspects of chemical drawing, property analysis and modelling within a consistent web site environment.

Investigation of percutaneous absorption of chemical compounds.

I plan to use the software to supplement classroom instruction in general and organic chemistry. We are currently unable to publish undergraduate student reports to the internet. We would certainly acknowledge contributions from this software in any work published.

Evaluate the properties of organic molecules. Calculate PKa etc. Help to design synthesis routes.

The software will be used to estimate solubility and other properties of organic compounds.

Research: We develop statistical methods for chemistry problems. We invent data mining methods. We are particulary good at a statistical technique, recursive partitioning. We compute chemical descriptors. We work on 3D pharmacophore identification. Teaching: We work with graduate students from Noth Carolina State University and the University of North Carolina. We work mainly on thesis problems. We have a number of publications in JCICS.

Analysis of structure and determination of logP

Predicted use as a tool for substructure search in various databases. This will be useful for (1) structure-based drug design, (2) search for unknown substrates for the newly discovered proteins from different genomics projects.

would like to have a look at the tools for our inhouse database of compounds.

I aim to identify and optimize small molecules as novel inhibitors of androgen receptors as potential anti-prostate cancer agents. I would like to request the academic licenses for (window XP platform): (1) The calculator plugins (such as pKa, lopP, logD and polar surface area) implemented in MarvinSketch. (2) License for Jchem. I will use these tools in my medicinal chemistry projects. I will use Jchem to manage an local chemical database. Thanks.

BioC/MicE 5309, Biocatalysis and Biodegradation class, taught completely over the internet. http://www.cbs.umn.edu/class/bioc/5309/idl/ University of Minnesota Biocatalysis/Biodegradation Database Pathway Prediction System. http://umbbd.ahc.umn.edu/predict/

Research — Mechanistic investigations of thymine dimer enzymatic repair

I am teaching chemistry with pupils about ESO

Teaching English students 11-18

Research is focused on chiral HPLC separation. Data mining, Pharmacophore, QSAR and molecular modeling techniques are used to epxlore the enantioselective recognition process.

I want to see substrate specificity of protease. so I need the program to explain structure- specificity relationship

I am m doing protein molecular modelling work. Before that,I need to get the partial charges Pka and polarizability results of some compunds.

I would like to use the tools in two aspects. The first will be for research. I currently work at a NIH-funded center that is interested in developing techniques for building block selection and diversity analysis of combinatorial libraries. The second aim is to teach undergraduates in an introductory organic chemistry course about cheminformatics and QSAR. This aspect will hopefully grow into an integrated part of the course.

current research interests: plant extracts and cell signaling. Use of plant products as alternative to antibiotics and anti-virals in livestock production. Program requires an understanding of chemical structure, identification of compounds of similar structure and predictive infor mation regarding chemical stability. Research will be published with outcomes have direct benefit to agricultural production.

Virtual screening of small molecule binding to RNA and protein targets

Screening of a large list of substances in sdf format for interesting candidates for a study of solvation behaviour.

I plan to use this software in my studies of chemical diversity analysis to assist chemistry graduate students in the planning of organic library synthesis. Furthermore, I also plan on using the software in my own research as a tool for chemical fragmentation for investigations into protein-ligand interactions via computational solvent mapping.

The software will be tested for using within the practical courses by students of Pharmacy. Generation of 3d molecules to get an impression of shape and properties of the inspected molecules. If it is able, the software will also be used for generating 2D and 3D structures for different databases. (www.wisda.de)

virtual drug database construction

I would like to use this package primarily as a visualization tool. I see its value for all levels of the chemistry taught at our college. It would be especially valuable to the organic and biochemistry students. The calculation plug-ins would also be valuable. In addition to traditional chemistry classes, I teach online chemistry classes. The web-based tools in this package would be ideal for online activities for the distance learning students. Students in traditional classes would benefti as well. I am the key person that helps other instructors adopt new technologies. If I am successful, then I will mentor other instructors in utilizing these great tools.

G-protein coupled receptors, QSAR

Work on effects and side effects of essential drugs. New focus on drug-protein interactions.

I am working in the field of modeling Structure-Activity Relationship with an intensive use of Machine Learning techniques. I need some of CHemaxon Tools to compute molecular descriptors.

To explain chemical subject in class, specially about how to calculate the chemical parameter

Retrosynthetic analysis Organic Lab reports

Molecular modelling, QSAR, QSPR models

Genome Biosciences R & D Projects: · Comparitive genomics in archae BACTERIA · Small molecular Data Base · H-fuel from cyanobacteria Comparative genomics: Explore life at the ultimate level of the whole organism instead of single genes or proteins. Understand by using the information found in the genomes of microbes, life’s simplest organisms, to study how proteins—the products of genes—carry out all activities of living cells, monitor environments to detect pollutants, protect citizenry from biological and chemical warfare, clean up toxic waste safely and efficiently. H-fuel from Cyanobacteria: Microbes thrive in every environment on earth, but the vast majorities DO NOT cause disease. Understanding them at a basic level will enable use of their diverse and sophisticated abilities. Develop new energy sources (biofuels). Identify Microbes that can be used for Energy and environmental cleanup activities: • Clean up toxic wastes • Capture excess carbon to help reduce global climate change • Generate clean energy sources (e.g., hydrogen) GBRI Small Molecule Database: With the inundation of novel proteins derived from genome database mining, transcript array profiling, and traditional biochemical approaches there is a tremendous need to develop more efficient methods for the discovery and optimization of small molecule ligands to help determine the biological function of these proteins. The objective of the project is to develop the capability to computationally generate structures comparable in quality to X-ray crystallographic structures but at a fraction of the cost and time. Develop technologies that allow extracting drug shape information from the dynamic trajectories calculated for modeled protein structures using virtual constructs. Identify and device technology that allows us to computationally prescreen small-molecule compound libraries containing many millions of structures in three dimension.

Starting to work on a new chemoinformatics project and therefore I like to get to know the state-of-the-art in this domain.

Prodrug Engineering

Recearch project is dedicated to molecular modeling of G-protein coupled receptors and rationalizing data on ligands’ interactions.

1. Evaluating for teaching chemistry 2. Our research includes virtual screening by SVM, docking and QSAR methods. The role of our group is to find natural compounds with potential anti-depression activity in cooperation with other departments of life sciences of the University of Tokushima.

Structure based drug modelling research

we intend to introduce molecular modelling to students who are yet not familiar with such software. In research we are especially interested in the calculation of properties.

I am post doc researcher in Anna Bernardi group. I’d like to use your tools for building combinatorial data base of Cholera toxin inhibitor.

The software will be used to determine Log P and Log D parameters of molecules that we are developing as inhibitors of a schistosomal cathepsin D enzyme. Molecules can also be inhibitors of plasmepsin II and will be tested against the malarial parasite. All research is strictly academic and will be the subject of several publications in the near future.

Preparation of scientific papers and reports on the therapeutic effects of drugs, the toxicity of foreign compounds and their metabolism. Basic reseearch into these topics.

I am about to embark upon an MSc in Chemoinformatics. I will undergo a research project that will involve new techniques for chemical structure searching algorithms. During my course I will be applying Java programming to a range of chemical related problems. My first degree involved the application of Genetic Algorithms to structure searching so I may pursue this further in my research. The exact details of my research have not yet been decided. The research will be conducted with a company but details of this can’t be provided at this time. I start my course on the 27th of September when more information regarding my research may be available. Thankyou!

Evaluating software for the purpose of relating pKa values and polar surface area values to water soluble species in petroleum products

drug design, screening

I’m personally involved in the development of new carbohydrates mimics that should bind to E-Selectin.

I need the structural details and properties of certain organic molecule, for my research which invovles synthesis and application of gold nanoparticles. I am trying to functionalise gold nanoparticles to construct a quantitative heavy metal ions sensor. I am also trying to understand the phenomenon of growth of nanoparticles. Both these aspects require structural, physical, and chemical data of organic molecules that are used as capping agents for stabilization of gold nanoparticles.

se implementara para alumnos de la carrera de bioquimica el uso de tecnologias de la informacion a traves de este programa con el fin de enseñar el uso de herramientas que le permitan usar los conceptos quimicos basicos. en el ambito de investigacion se usara este programa con el fin de analizar macromoleculas y sus reacciones que participen de la via glicolitica.

Main objective of our research is the assessment of the environmental behavior and fate of contaminants at contaminated site at a large scale. Teching activities comprises human health and ecological risk assessment lectures and the development of conceptual site models.

Understand how users comprehend large chemical models.

We are having our bioinformatics laboratory which includes some bioinformatics and cheminformatics tools. We wish to construct a local database of small molecules which are freely available from web as well as the molecules developped from our department during research work. So in this connection we would be using your jchem package. In addition to that I am doing a research work in “Development of drug molecule for Lymphatic filariasis” in VCRC (Vector Control Research Centre, Pondicherry, a WHO collaborative research centre under control of India Council of Medical Research) VCRC profile can be found in following website:(My research head is Dr.K.Balaraman) vcrc@vsnl.com In this work i will use your marvinsketch for finding molecular descriptors and drawing some leads for searching

I teach Biophysics. I teach students of medicine, stomatology and pharmacy. The area of my research are the interactions of plyphenolic compounds with bilogical and artificial lipid membranes, using a cuple of methods (microcalorimetry, EPR, spectroscopy etc.). I would like to use the molecular modelling methods in my research.

Seems like a nice viewer for looking at molecule structures

Sir, your software package is used only for teaching & research purpose only. Your software is very much usefull in calculating pK parameters. Thank you

We are very curious about all your tools. The depiction capabilities are quite good as well as the fast search methods for databases.

analysis of QSAR properties of organics compounds

In this study, the crystal structureof an enzyme from Plasmodium falciparum is employed as target for ligand discovery. The primary goal was to use rational design approaches to develop novel inhibitors to this enzyme, and to perform subsequent in vitro screening against the recombinant protein. The rationally designed ligands needs to clustered now to determine a few core structures to use in the in vitro screening against the recombinant protein.

doing the virtual screening

Bioinformatics training at MSc level. Project students research projects.

We are currently performing several whole organism high-throughput screens (HTS) using ~250,000 diverse small molecules of drug-like and natural product-like small molecules in the Institute of Chemistry and Cell Biology (ICCB) collection at Harvard Medical School. To date, we have identified highly active molecules by HTS in the ICCB collection. We would now like to use the Jclustor tool of JChem for clustering, diversity calculation and library comparisons to sort these large numbers of compounds identified in our HTS(s) that need to be rapidly analyzed.

organic chemistry natural product chemistry

research implementation about screening databases and calculating descriptors and generating databases

monolayer

Your software will be used in order to create a number of chemical descriptors to be used in the construction of Quantitative Structure-Activity Relationships (QSARs). At present our research group is involved in creating QSARs for placental transport, skin permeability, melting point prediction and blood-testis barrier permeation.

Pubblications

study the structure, function and kinetic of C-24 sterol methyltransferase

I am in a feasible project to find new drug scaffold for CNS stimulation. I am also interested to use the plant as the sources for drug production.

constructed titration curves, bond chemistry, solutions, polymers

I am currently an instructor for chemistry teachers in the french speaking part of Switzerland. I try to develop programs in Java 3D for chemistry education. I have not fully tested, for the time beeing, your MarwinSketch and MarwinView but I hope to be able to do so very soon. I shall attend the ChemAxon user Group meeting in a few days in Budapest.

We intend to compare our newly developed molecule descriptons methods with the state-of-the-art methods.

Biochemistry

I wanna show my studens how usefull is to apply the tools implemented in the software. Addiotionally, I want to use this tools for my own research

Edit and maintain molecular databases under Linux. Quickly estimate phys-chem parameters. Convert between mol. formats Visualize compound libraries.

This application will enhance what is taught in the classroom.

Will be using for similarity calculation along with teaching

tutorials for undergraduated students

I would like to calculate some properties of a natural compunds family, log P and some other descriptors to correlate them with biological activity.

I would like to use JChem tools for my work on virtual screening.

Analysis

I would like to incorporate accurate structures and modeling into my general chemistry, organic chemistry, and biochemistry courses. I am eager to adopt a software that is user friendly while maintaining accuracy.

We are running the database, Biosilico. It is a web-based database system that faciliates the researh and analysis of metabolic pathways. JChem, one of components, plays a role in searching the chmical structure. In addition, we use Biosilico in a teaching curriculum for bioinformatics.

Prediction pKa Teaching medicinal chemistry course

We will be using the tools to attempt to “grow” compounds that are readily synthesized.

creating a drug database

Development and delivery of online learning for chemistry students

Building electrostatically self-assembled thin films using polyelectrolytes. Need prediction software to predict pKa, charge, etc. of polymers and small molecules to be used in thin film assembly.

To supplement the teaching of physico-chemical proerties of drugs.

I generally use SMILES for structural analysis and would be interested in using the molecular descriptors available from Chemaxon. I would need to investigate the software more thoroughly in order to find out further potential uses in my research.

My research work concentrates on the borad area of molecular recognition phenomena. The interaction of small moelcular systems have been studied well. However, the level of understanding of the biomolecular interaction at the molecular level is not good. To start such type of work, I need this partocular software. Although there are many such softwares, I find this has many options and would be helpful.

We will be using this software to supplement the Organic Laboratory exercises.

to build moleculs and use to teach in the clasroom

Drawing Drug Structures for Medicinal Chemistry Courses

I may use it to draw chemical species to include in research papers or other presentations. It is also being considered for implementation into a chemical database so that the structure of the species can be displayed and manipulated. The pKa tool may also be of interest in dealing with solution phase reaction mechanism generation. The pKa tool may give a general idea of what the equilibria of reactive intermediates may be, though I am interested in how these predictions are made.

I am working on pharmacophore generation and evauation and CADD for new drug discovery and lead optimization. I am planning to use chemaxon for analyze my pharmacophore results by using logP and H-bond donar/acceptor (lepenswki’s rules)

I would like to use chemaxon software for teaching chemoinformatics to students pursuing their PhD in chemistry affiliated to University of Pune. I would like to explore the possibility of using the chemaxon tools to generate molecular properties in a distributed computing environment. We developed distributed search environment (ChemXtreme) where computing application will be tested using these tools.

STRUCTURAL CHARACTERIZATION OF PROTEINS INVOLVED IN DISEASES. MY INTEREST IN YOUR SOFTWARE WOULD BE TO EVALUATE THE CHEMICAL CHARACTERISTICS OF COMPOUNDS HAVE BEEN DESCRIBED WITH PARTICULAR BIOLOGICAL ACTIVITIES AGAINST THESE PROTEINS

hetrocyclic chemistry of indoles & oxindols. Anti parkinson drugs.

Evaluating the physical and chemical properties of diisocyantes and known inhibitors of the enzyme GGT for doctoral dissertation.

Research: Edit/visualize molecules, property calculations, management of virtual library

…to be used on General Chemistry Online (http://www.generalchemistryonline.com), a free educational site, to augment new segments on bonding and solid structure, and to replace Chime in the Common Compound Library.

I will use it as a visualization tool for my elementary bonding analysis.

I teach a senior-level courses in cellular and molecular biology and molecular genetics. Marvin Sketch and Viewer will be useful in drawing structures for these lectures.

We are synthesizing small organic molecules and evaluating their properies as ion channels and carriers.

ChemAxon Software is to be used within the Computational Chemistry and Molecular Modeling Laboratory oF SOP/WVU, http://www.hsc.wvu.edu/sop/compchem/index.htm as a visual aid to the course Pharmacy #780 (Introduction to Molecular Modeling).

We are developing new bioanalytical methods for quantification of mostly antimalarial drugs. pKa, log P etc will be used for method development purposes and cited correctly once the assay is published.

I plan to use the ChemAxon tools for the purposes of my Ph.D. research. The goal is to use JChem and other ChemAxon tools for the analyses of chemical datasets and the development of my own algorithms and workflows for chemical data exploration.

Use to teach chemoinformatics to postgraduate students. In the future, PhD students might be interested in using the software in their research (no plans at this time).

I am a Principal of the Foundation for Chemistry. The Foundation for Chemistry is a consortium of Scientists conducting research in Organic and Medicinal Chemistry and Material Science. The Foundation offers expertise in Organic, Medicinal, Polymer and Computational Chemistry. In silico tools include molecular orbital and molecular mechanics applications and molecular docking tools The Foundation has developed a new paradigm for similarity transforms and has published extensively in Qualitative Structure-Activity Relationships and Qualitative-Structure Property Relationships. The Foundation is an unfunded, no budget and non-profit organization We fully comply with all of the requirements of academic software licenses.

I will use the tool for my research on quantitative structure retention relationship.

we are currently a small group of 15 chemists and 15 biologists working towards finding new medication for pain and obesity. The research is based on the canabinoid receptors in brain which could be used as a target to change the chemistry of emotions!!!!

calculating and designing the DNA and base pair

I like to use the pKa calculation package to predict pKa values of the organic compounds I am synthesizing in the lab.

General structure drawing tool for lecture overheads, for preparing handouts for lab classes, etc.

I will be using this for my research work.

I am to evaluate these tools for undergrads & postgrads training in order to develop their skills in computational chemistry.

I would like to see the database system implemented via JChem to compare to that available via MDL. It may be used in a chemoinformatic class for MedChem students to show them the type of software commonly found in industry for searching chemical databases. In terms of research, a large number of chemical structures need to be stored and easily accessed in my research.

Will use for on-line teaching for general chemistry and physical chemistry.

I would like to provide molecular models for my IB teaching and draw structures to import into my classroom notes

I am a student looking for a program to draw structures.

The software will be used for lectures and exams in my chemical biology class. Chemical structures will be drawn. Also need visualization of protein-ligand binding, pKa caluclations.

Organic Chemistry *Photocatalysis. Enantioselective catalysis

Testing things

I require the pKa plugin to estimate the protonation states. They will be used for Gibbs free energy computation to get equlibrium constants. They will be used to study the thermodynamic feasibilty of large metabolic networks.

NMR analysis of sesquiterpenes and other organic compounds

computer aided drug designing

The NIH Chemical Genomics Center is a component of the NIH Roadmap initiative. We are a non-profit center that aims to create small molecule probes for use in the study of biological systems. During this process, we are screening a small molecule library against a diverse set of cell-based and enzymatic assays. We will be following up compound series of interests to further optimize potency and solubility. All data and work done at the center will be freely available to the public via NIH database PubChem and via our website. One that makes us unique is that we’ll be depositing over a million dose response curve data as part of our primary screening campaign. ChemAxon software will be used througout all aspects of chemistry. We’d like to use your tools for public web-based access to our repository of data. We’re interested in contributing all customization and code we build inhouse to the general community. We would also be interested in citing your software in our work.

I intend to build an internal website for managing HTS screening data and chemical structures. It will be based on a MySQL database with a web front end. Marvin & JChem tools will be used for viewing and searching the database. This will be an internal website used by the Bogyo lab (http://bogyolab.stanford.edu).

I have not yet examined the full capacity of the software to be able to tell how to implement all aspects of use. I am certain that the software will be useful for teaching and research in Biochemistry and Medicinal Chemistry, which are my fields of interest.

The main goal of the use of your software is the possibility to show to people in my group how to build structure, database and how to use it to make a structural search based on different criteria. I am part of a new group in chemoinformatic at CBS in Denmark and I would like to test also the software on my own and personnal work in the chemoinformatic area.

1. Study biochemical structure and properties of bacterial cell envelope. 2. Study chemical nature of molecules involved in cell-cell signaling and communication.

The research focus lies in the determination of 3-dimensional biomacromolecule structures, de novo structures as well as structures of complexes. In this matter we would like to obtain structures with small fragments which we would like to derive by fragmenting drug-like and ligand-like libraries. We would like to use Fragmenter to obtain these small fragments.

Firstly, our school opens a course for the under-graduate students, with the name of “Design of Drug Molecule”, which the primary lecturer is the administrator of our group. So we need to prepare some materials for the lesson. However, we cannot afford the expensive software commercially available. ChemAxon’s Academic Package is the best choice for us. It not only offer free access for academic institute, but is a powerful and useful tool to learn and understand drug design. After the lesson , we would select several good paper for further research. Secondly, Our group has gained several compounds from a natural plant recently, but the amount is so few that it is impossible for further property study. So we want to investigate the physiochemical properties of these compounds via theoretical computing, other than experimental ways. As a computational software, ChemAxon’s Academic Package meets our requirement well. For these two reasons, we ask for your agreement on our using this Academic Package. Many thanks and we are looking forward to your response! Best regards!

I would like to learn how to do virtual screening and virtual synthesis.

high school and pre-university chemistry. I want to incorporate it in an e-learning environment.

computer drug design computer docking

I have been using AutoDock to virtual screen the National Cancer Institute Database for a collaborator at Rockefeller University. I’d like to use the chemaxon software to search for similar compounds in other databases.

We currently operate a small research laboratory employing several graduate students. Our principle aim is development of novel pharmaceutical compounds for treatment of tropical diseases, cancer and HIV. We hope to use your tools to store and manage information regarding these compounds. Another aspect of our lab involves teaching and training of undergraduate students. We plan to enable a web application allowing these students to learn more about the research in our laboratory.

Would use software for evaluation of structures used as inhibitors in a biochemical screen.

Retrosynthetic synthesis for educational purposes.

Multidrug resistance and modulation

undergraduate and graduate teaching

master courses on chemoinformatics, see http://infochimie.u-strasbg.fr/master/master_home.htm

Evaluation and design of taste ligands

I intend to use the software for research into ligand interactions with macromolecules. My field of research is protein crystallography with a theme in Bioremediation.

1. teaching structural biology to junior college students 2. constructing small molecule ligands for protein crystallography

My main interest is to evaluate the software for teaching purpose. In particular, It will be used to illustrate some aspects of virtual screening procedures and their applications in chemical genomics and drug discovery. Furthermore, I would be interested to evaluate the software for research as well.

Work on salivary amylase enzyme catalysis and biofilm enzyme agents

I use this tool to design 3D models of ligands or modified side chains of amino acids in a protein for molecular modelling.

X-ray crystallography-based drug design

In the development of affinity chromatography, several strategies could be taken into account, such as protein (protein A chromatography), peptide, enzyme inhibitor and so on. In our work, high-troughout screening of ligand from small molecules will be carried out on the basis of log P, pKa and structural similarity. Therefore, a software is very important for our research. On the other hand, this software will be applied in the coure of Drug Discovery and Design.

I am doing my final thesis creating a prediction method for pH dependent solubility. For this purpose I wish to predict pKa values and intend to use the cxcalc pka plugin.

I am currently attempting to develop a GA/ANN/QSAR model of the human uridine diphosphate glucuronosyltransferases under the aegis of Anna Radominska-Pandya, who is one of the leaders in the field, and the developer of the current standard method of glucuronidation biochemical assay. After that, I plan to broaden the methodology so as to both map the active sites and map the enzymes in substrate chemical space. After that, who knows, empirically driven AI-based protein-folding predictive software? I have collected and am in the process of collecting much data from the literature and from Dr. Radominska-Pandya’s unpublished findings. You know, all those little trial experiments that never went anywhere, so you stopped them to avoid throwing money down the sink, or didn’t want to be distracted from something more productive? Well, even drops of water add up after twenty or thirty years. I don’t know why I’ve fallen in love with data. I have a sort of tolerance-hate (no, not love-hate) relationship with computers. In fact, I’m not even any good with math. If you let me use your software, I’m sure that it will go a long way toward my being able to publish at least ten good papers while still in graduate school. With that kind of assistance, I would be exceedingly grateful, and would advertise your product shamelessly:)

high school teacher of chemistry

teaching: visualization of stereoselective reactions research: visualization of polymers. mechanisms of controlled radical polymerization

We realize a web application which allows to index the molecules availables in the french academic labs. For each molecule, we would like to calculate chemical properties by ChemAxon tools .

QSAR/QSPR models building

Biochemistry of plant defense reactions, phenylpropanoid metabolism, fatty acid metabolism, chemical signalling

steroids and amino acids, capillary electrophoresis

Computer-aided drug design; QSAR; Molecular Modeling and Simulations.

Creation of a small database or organic compounds to be tested in-vitro against a target, for academic use. Need to filter commercial database.

Used to visualise and compare a library of virtual ligands built to fit a set of protein cavities.

Analysis of substrate similarities vis-a-vis binding site local structural similarities for specific protein families.

I teach chemistry and I would like to try your software in my chemistry classes. But first I would like to see how easy it is to use with students (age between 16 and 19 years old). Then I will use the software for drawing some organic molecules in class or for the laboratory practice.

Principally teaching, with perhaps occasional research use. See my web site – http://ed.augie.edu/~viste/ and the presentaton listed there Exploring Chemsoft Software Ernst J. Schumacher, Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012 Berne, Switzerland and Arlen Viste, Department of Chemistry, Augustana College, Sioux Falls, SD 57197 Presented at the 228th national meeting of the American Chemical Society Philadelphia, PA 25 August 2004 I think that ChemAxon tools may be useful at our upper division levels. Alex Allardyce encouraged me to submit this application.

I am developing an academic website where students can research the foundations of science. To find help them deterine the validity of current techings by investigating the origins of those discovries. This wiki site will attempt to provide supporting information for all of its pages funneling down to the fundamental axioms of science.

– Investigation of intestinal absorption of drugs – Correlation between physicochemical properties and fraction absorbed

I teach in a course of General Physiology and I develop basics for Chemical-Physical proprties of biochemical and organic molecules. In my research often I need to determine structural and functional characters of short peptides and drugs.

Drug design class

Drugs semisynthesis from natural products

We are running the M.Tech. program in Bioinformaics since 2002 and the B.Tech. program in Bioinformatics since 2003. The programs have the strongest curriculum & syllabi. Research in progress on Drug Discovery & Development and Biological & chemical Database development.

Our research group studies interaction of various tuberculostatics with biomembranes. We intend to use mostly logP, logD and pKa prediction modules for the drugs we study.

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I am teaching a new course on chemioinformatics and would like to use the programs for demonstrations

The software will be used for a summer student to draw molecules for a report on his reserch project.

Oceanography

I study protein receptor and pharmcophore ligand, we want use the Chemaxon package to develop Web application.

I do statistical research on bioinformatics and chemical informatic topics. I create methods for the analysis of HTS data. I study chemical diversity. I’m also an adjunct statistics professor at North Carolina State University where I direct thesis work of graduate students.

Evaluation of structure-activity properties, hydrophobic surfaces, solvent accessible surfaces, molecular shapes, local polarity, and overall hydrophobicity, both in research and in classroom presentations.

Produce notes for pasting in research notebooks, and figures for publication. We also do a regular “mechanism club” where problems are posted for general consumption and edification.

I’m interested in an initial evaluation of the capabilities of Marvin, in particular the visualisation of pdb/mol2 files in 2D and the property prediction modules. I will not be used as part of my teaching committments.

We need this software for academic research. We are working non-profit research institute. We need to use this software to develop web tools for classifying small chemicals our service will be free for public. With Regards Raghava

Package will be evaluated for use in small molecule interactions with prostate and breast cancer proteins.

For teaching students in chemistry lab

Our research involves the generation of novel molecules using graph theory and estimation of thermodynamic properties of these molecules using group contribution theory. We use the program to estimate the ionic form of the molecules at a standard pH near 7.

Bioinformatics searhes

I’d like to use this software for evaluation of chemical properties to predict reaction behaviours.

Molecular Modeling

to convert the name of a chemical compund to chemical structure

Using OWL, so it will help to have the Marvinsketch and associated programs available.

These softwares will be at Computational Chemistry classes. In there, they will be used to ilustrate chemical principles, reactivity and molecular design. In research, they will be used to prepare presentations and to ilustrate chemical principles on Molecular Modelling.

I would like to calculate the log P, log D, pKa etc. as parameter to predict formulation development.

We are engaged in determining the structures of carcinogenic molecules bound to DNA. The primary use of the software will be for preparing figures for publication and presentation.

I will be using the product for predicting the brain distribution of novel nicotinic antagonists we are creating for a large NIH center grant. THe primary hypothesis is that a nicotinic antagonist which partitions to brain will be able to reduce the positive reinforcing effect sof nicotine. We have already published a number of papers on the chemistry of the compounds. However, we would now like to be able to predict brain distribution of the nicotinic antagonist prior to in vivo testing. Specifically, I need to evaluate LogD, LogP, polar surface and hydrogen acceptance to make accurate predictions of in vivo pharmacokinwtic organ distribution. I have two graduate students now working on brain distribution of the compounds and as such this program will be highly valuable. With regard to teaching using the program, I will use it with my current students and the two new students I am bringing in Fall of 2006. Students recieve a Ph.D. in Pharmaceutical sciences and as such they typically work in industrial settings upon graduation.

We are associated to the university of Rimouski (UQAR) for some of our research. This application will be very useful for the installation of an inventory system for our chemicals products. Thanks you to all your team.

QSAR on P-gp substrates

Interested in using MarvinView pka and charge tools for ligands in the RCSB protein data bank website. These tools will be used prior to docking ligands and running Molecular Dynamics.

TO be used in Chemistry general chemistry and organic chemistry lecture and lab. Since I am designing P Chem lab, this will also be implemented in the lab. For research, it can serve a start point for input geometry.

We are currently developing a new method for the calculation of Gibbs energies for enzyme-catalyzed reactions. For this purpose, we need a pKa prediction module.

We will use your software mainly for the visualization of chemical (sub-)structures at this stage of our research. Since we are working on activity predicition of small molecules we are interested in finding common substructures and lateron derive mechanistic conclusions. Your software will be used to help in the interpretation of the results. At the moment part of this work is carried out by students as part of their diploma thesis. Further inclusion in selected lecture chapters is intended.

To be used in conjunction with High-throughput screening for the development of new anti-tubercular agents by using a novel enzyme target in TB. To be used to search for pharmacophores from a previous HTS study, then the use of that pharmacophore in a virtual screen of a larger compound library.

Communication of chemical structures and training for structure-based search engines.

I am intetested in using the partial charge evaluator package to investigate the hydrogen bonding capacity of various osmolyte structures. I wish to correlate osmolyte hydrogen bonding to their thermodynamic characteristics.

This is to estimate the hydrolysis rate of disinfection byproducts

Will be used to evaluate the properties of combinatorial library members to determine drug-likeness

To show students in Biology and Chemistry the attachment of bonds on chemical compounds.

to use the tools for predicting the activity changes in the mutant forms of detoxification enzymes from patients

I will use this software for my research. It is a total synthesis of alkaloids. It will help me for predict the physical-chemical properties of my products.

Investigating using the chemaxon results as features for other machine learning techniques.

I am interested to improve the prediction of some kovats Index of compounds that are not available as standards or cited in tables or bibliography.

My aim for this software is to introduce and educate fellow postgraduate and undergrauate students on the use and usefulness of chemical software in research. I will be concentrating on the physicochemical parameters, like CLogP and pKa, in particular their calculation and importance for pharmaceutical sciences. For research purposes I will compare this software package to other packages used in modelling compounds and for calculating physicochemical parameters.

synthetic organic photochemistry photoinduced electron transfer time-resolved UV-Vis spectroscopy fluorescence spectroscopy

We will evaluate it for many applications. Firstly we will evaluate the substructure seach and the building tools. Furthermore we will use the pKa calculator and also evaluate the other tools.

Metabolic Prediction: representing common chemical subgraphs in smart notation

I teach Organic Chemistry I and II and would like to introduce students to the concepts of retrosynthesis and drug design as a way of showing that the basic reactions are building blocks in modern synthesis.

This software will be used in my Medicinal Chemistry classes to develop data for QSAR studies. Also, I may use the software for another course during short term (a short class in January) to make some estimations on drug properties and development. Also, I could use this software in an organic course to teach tautomerization, where students can compare there answers to the correct answers generated by this program. If you know of any specific applications of this program and QSAR, please pass it on to me, as these would add to my applications. Thanks.

Research in Biochemistry and Biological Sciences

Using the Chemical Inventory database system to keep a track of research chemicals.

We want to do docking-based VS and want to explore chemaxon tools capabilities. Ideally, docking input and output files would be stored in MySQL database and Chemaxon suite of programs would be used to provide all cheminformatics needs and link to the database.

Personal study

from the website we know that chemaxon is a powerful software package, especially in drug design. we are very interested in it. even if we have some commertial software such as SYBYL, but it is too expensive, we have just a few modules.however we can’t develop new software, for the ability is limit. Then we were so happy to find your software package, Thanks for your technical support!

Database of commercialy drug like coumpounds. Database of humanGPCR and ligands. Database of scaffolds …

We aim at building a local database of commercialy available compounds for screening allowing us to selected the best compounds to be tested in the assays available in our institution related to neglected diseases such as leishmaniasis, tuberculosis, malaria , chagas’disease, schistosomiasis. Calculated properties will be used to guide the selection of compounds and together with the biological results, to perform QSAR studies and buid prediction models. Screening and chemical data will be stored in the database. Marvin will be used to draw and visualize structures. Apropriate derivatives will be planed using REACTOR and FRAGMENTER. The later will also be used to build databases to detect privileged fragments and help in the hits to lead development.

I will evaluating the soft for my lessons industrial chemistry. thanks,

I wanna use it to get the pka of the micromolecule

We are located in a Faculty of Pharmacy. We aim at given our students access to various chemoinformatics platforms for -practical experiments in chemistry to evaluate in-silico parameters of the compounds they synthesize or analyze -case-studies on marketed drugs to evaluate in-silico parameters of the compounds they study As teachers, we want to give them examples of chemo-informatics tools during classes. Our research team is a team that is co-administrated by the following Academic and Public Institutions : Pasteur Institute of Lille, INSERM, University of Lille2. As for research, we are gathering several tools, among which ChemAxon, to evaluate some in-silico data of our chemical libraries of bioactive compounds. These data are aimed at being used by the medicinal chemist to rationalize SAR data.

I would like to use it in similarity&diversity analysis, clustering, virtual screening and to compute molecules properties.

2-phenylbenizmidazole

for drug design use

Drawing chemical structures and sharing of analysis of research products and intermediates.

Nucleic acid structure and function. Enzymology of nucleic acids, including substrate recognition and modelling.

high throughput screening. drug discovery in neurodegenerative diseases.

The project is aimed at computer-aided lead discovery and drug development in which your software is implemented in screening methods and for the creation of molecules in a database.

I need a nice drawing tools for a presentation. My colleague Krisztina Boda recommended me ChemAxon software.

Teaching of Biochemistry. I would like to use the soft to supplement classes and activities of students

Teaching biology and Chemistry in Danish Gymnasium

We will be using your software with the Chemical Inventory Software developed by Dann Vestergaard & Claus Stie Kallesøe Their inventory project seems to rely on your project so I would like to use both together for chemical inventory and safety management for first our department and then possibly our full university

Cheminformatics, particularly QSPR models for ADMET properties.

for viewing chemical libraries

Preparation of 3D representations of molecules for docking with GOLD

We are testing systems to us in our research lab.

New drug development for protection against neurodegeneration (Alzheimer’s disease and stroke). Molecular mechanisms of neuroprotection. Genetic engineering as a tool for studying novel growth factors. Neuropeptide-based drug design associated with impotence. Neuropeptides and cell growth – drug design against cancer.

working on drug discovery synthesis

Main aspects involve using the Calculator plug-ins and Jchem and similar research tools to aid anti-cancer drug-design process for academic purposes.

Using for describing superplasticizers in Self-Compacting Concrete.

Free time study of chemistry and preparation for university.

I’m looking for new nicotinic agonists.

I would like to try to implement it into our homemade chemical inevntory database

We will use these softwares mainly for do conformational analysis and to teach computational quantum chemistry.

to teach chemistry up to Adanced level for university entrance

Estructura y caracteristicas fisicoquimicas de peptidos beta-amiloide y bicapas fosfolipidicas.

Want to find out the known natural compounds structure and use as a database for public access with biological information supplied based on the literature.

predicting LogD, pKa and LogP, QSAR

diploma thesis: combinatorial library for drug design.

This software is to be evaluated as a platform independent replacement for Cambridgesoft database software. It would serve as inventory management with structural search capability. It would be nice if a connection to a mysql db could store spectral info as well as structure.

To create MDL files

we using chromatic lipid-mimetic polymer polydiacetylene – Biosensor, for predicting the extent of interaction and permeation of pharmaceutical compounds through lipid layers.

Research the relationships between Structure and mutagenic and/or cancinogenic activity Teaching General chemistry in environmental studies

We will be using your tools to help us prioritize data from our neurodegenerative disease drug discovery efforts using our inhouse HTS system and data generated by Teranode Design Suite software for biological data analysis and record keeping.

Isotope fractionation effects as a result of logP values

Used for determining chemical properties of bioactive molecules.

- introduction of the computation methods in undergraduate calsses

I will be using ChemAxon to assess the structural relationship of small molecules which I have identified as “interesting” in my research. I have conducted a high throughtput screen here at HMS and need a tool to aid in the chemical analysis component of the research.

a elemental course in medical chemistry

data integration

I am very interested to give to the students the tools to understand important chemical aspects related to the properties of several drugs, pollulants and other xenobiotics and the possibility to predict different properties related to the action in the human body of these compounds. In other hand, I am very interested to predict chemical properties from different toxics to implement the correct analytical techniques to investigate these substances in biological matrices.

quantum mechanical study involving triethylphospate and di-fluoro stubstituted version

Teaching of Chemistry (Organic, Inorganic, polymers etc) Computer-Chemistry, Use of Chemical Information Systems etc *** We want to evaluate your software first before we can give a description of the implementation

Marvin software help me to plan my syntheses. Mainly I use marvin sketch and its plugins (pka, molecular weight etc.) Sometimes marvin spaces is needed. In future we plan to start laboratory database of chemicals. We plan to use chemicalinventory.org software which is based on JChem.

we hope to use this software for research in the peptide and protein field, and for project students teaching

medicinal chemistry relate to QSAR

I am developing a tool to generate ligands using genetic algorithms. I am interested in using ChemAxon products in fitness function evaluation.

Key stage 4 molecular models

For a molecular modeling class project

I realize docking experiments because I want to apply SAR by NMR strategy to design ligands with high affinity for DNA polymerases.

I want to create molecules and I was told that this is a good tool.

Molecular modeling and QSAR

We are collecting a large dataset of peptide derivative affinities for biogenic amine receptors. My aim is to generate pharmacophore models based on the structures of the ligands to direct design of second generation libraries of non-peptide compounds.

I work in an academic HTS lab. I am interested primarily in molconvert as I deal primarily with SD files supplied by compound vendors, but I would like to convert them to SMILES format.

research of ligands for CA-CYP51, analogs of ketoconazole, study of docking, pharmacofore and synthesis. research of pharmacofore of AD1 receptor, docking of PARP and IDO ligands

I am working on developing predictive methods for organic compounds based on group contribution and topological indices.

research in the medicinal chemistry. for accesing qsar and property access

To evaluate the use of this software in prediction of physico-chemical properties of molecules.

We are interested in platform-independent drawing and visualization tools, as well as in tools for library design and analysis/processing of hitlists coming from virtual screening (diversity, common substructures,…). Programs will be used in advanced lectures, by diploma and PhD students, and for own research. We are also looking forward to see the ChemAxon components for PipelinePilot.

Student tutorials in general chemistry

Diploma thesis about Caco-2, Blood-brain-barrier and solubility. Use will be focused on molconvert and cxcalc’s psa plugin.

Teaching: Introduce students on Organic Chemistry and Advanced Organic Chemistry to computational methods. Research: Develop new reaction models.

Molecular modeling, Planning of Drugs, Construction of new molecules.

I’m interested in molecular diversity and clusterization, in particular. We work in the field of QSAR and 3DQSAR.

My aim is to study molecular modelling and quantum mechanical calculations of small moleculae compounds

Heme proteins function

Analysis of molecular diversity

Database support for virtual and physical screening efforts.

This software will be used for my research. It appears that your software will compliment our data obtained from LC-MS/MS analysis. Also, I will require your software’s ability to generate IUPAC nomenclature to aid us with our manuscript.

drug designing for cancer QSAR research We conduct National Level Workshop on Bioinformatics

for lectures on Molecular Modelling and Computer-Aided Molecular Design

Studies on antimicrobial RNases. Interaction with bacteria cell wall components

Our group (The Molecular Design Group) is involved in utilising a wide variety of Computational Drug Discovery (Virtual Screening) techniques to aid in the search for novel lead candidates of targets such as Nuclear Hormone Receptors, GPCRs, Anti-tubulin and HSP90. Chemaxons tools would be key in this screening process and importantly in lead optimisation of identified hits.

i have to write labreports for my study, so i need a program to draw chemistry on my pc.

I am engaged in a variety of clinical and pre-clinical research projects in the area of Clinical Pharmacology. My research involves a good deal of analytical chemistry and I often need to draw chemical structures and do various calculations based on the chemistry of the drugs and metabolites that I study. The chemical structures will also be used in presentations and publications in the future.

I would like to see this software incorporated into our organic chemistry courses and higher. In addition, the faculty will also find this very useful in certain research applications.

pKa calculations for isolation of natural products.

Software will be used for drawing plant metabolites, natural products and other small molecules for publications, presentations and internal lab record keeping.

calculating pKas relate structure and acidity

We develop new ligands which are acidic and the tools will allow us to predict pKa. Further, we can use this same software to allow students to make educated guesses about molecules they might come across in class.

I will use Cheaxom software on my D.Sc. thesis research.

We plan to use your software in Organic Chemistry classes.

To prodice material for use in lessons for students aged 13-18 in particular Also possibly placing material on the Innternet to help students with their studies outside of the school environment

setting up initial software for a computational chemistry/modelling lab and for biochem and medicinal chem pharmacy courses

I will be using this software to predict the pI for a compound that I am trying to purify with an anion exchange column for pretargeted radioimmunotherapy application.

Environmental risk assesment for chemicals (pesticides) based on QSAR analysis.

Conversion of SMILES into sdf files

General laboratory use, tool for docking studies

in order to research and improve the chemical structure search, I’d like to have some open resouce application softwares such as Jchem, and supply my student with these softwares to do research on structure search and implementaion. thank you very much!

for evaluation

We want to test and perhaps use a chemical inventory software which needs the Chemaxon software.

we will be using the chemaxon product in our labs primarily for teaching students ,the computational cheminformtics implementation . we feel the live exmaple of chemaxon shall be best suited for our students

QSAR-QSPR modelling and reaction classification

teaching chemistry through softwares. display of molecules, various models, conformations, calculation of molecular descriptors, simulation of spectra, reaction kinetics calculation, molecular modelling, drug designing, energy minimisation, chemical database searching, reaction pathways, quantum mechanical calculations, pharmacophore identification, docking, sequnce analysis etc.

We conduct chemical genetics approaches, using automated screening of chemical libraries and cell-based assays, in order to isolate new compounds that could be tools for resarch. In this aim, we use an information system, called phenoscreen, that has been developped by CEA computer scientists (namely S. Roy and C. Charavay). Phenoscreen uses, for the compounds represntatin, some chemaxon’s products.

exploring 3d java graphics

Tools to be evaluated for use on undergraduate courses in medicinal and pharmaceutical chemistry.

We are working on various aspects of human nutrition, lipid biochemistry and gastroenterology, with a particular interest in cancer. The software will help us a lot for Pka, log P and log D calculations.

Use of Phenoscreen software developped by S. Roy and C. Charravay from CEA Grenoble

Construction and study of different organic ligands. Searching of different conformers of organic compounds for structure-activity dependence revealing. Potential surfaces analyzing for purposes described above.

organic chemistry

Teaching: drug design course for pharmacy students, molecular modeling course for material science students. Research: a number of studies involving QSAR, toxicity predictions, molecular docking.

i’m doing my graduate in organic chemistry and i’m looking for useful software.

development of small molecule inhibitors of kinases for the treatment of neurodegenerative diseases

I hope to use chemaxon for browsing/visualising chemical files and for computing descriptors. If it is user-friendly, I will use it to teach/visualise basic chemistry.

For about a hundred chemicals (IUPAC name) I would like to observe their structure and analyze this through Prolog computer program.

Teachning Chemistry an biochemistry

We plan to use Jchem’s search toolbox to assist us in developing a program that combinatorially generates small molecules that act as ligands for proteins. These small molecules will act as drug precursors that will undergo further testing.

I am trained my student to study and compare the file formats, and it is hard to find one support RGfiles that is suitable for a group of compounds of the same scaffold but with various alternative groups. If this package is good, I will continue to implement a web site for scaffold searching system…

We are trying to arrive at a QSAR for the 40 sets of compounds whose chemical structure and activity has been evaluated by us.

We are a non-profit, catholic school in BRAZIL. We intend to use your software in class with our chemistry teachers. I’m the IT manager of the institution and I’m making this request on behalf of the Chemistry teachers and the school principal.

We group of Molecular Modeling at IICT want to use your products completely for research purpose.

Sensory science; electronic tongue; Teach students organic chemistry and inorganic chemistry;

Reserch on Biocomposite materials and disermination of research results through publications, seminars and teaching.

I am dealing with 1. visualisation of small and macromolecule. 2. Database maintaining system 3. Clustering and visualisation kit 4. Molecular descriptor 5. Virtual screening 6. Tool related to molecular modelling and drug design

I want to use ChemAxon to assist my research. For example, managing of my data, do some precalculation, and so on.

The Medical Structural Genomics of Pathogenic Protozoa (MSGPP) group studies the protozoa that cause malaria, sleeping sickness, leishmaniasis, Chagas’s disease, toxoplasmosis, cryptosporidiosis, amebiasis and giardiasis. MSGPP, directed by Dr. Wim Hol, determines structures of pathogen proteins with ligands bound, to aid in the process of drug design. MSGPP uses cocktails of potential ligand fragments and whole ligands such as known inhibitors and substrate analogs. MSGPP is looking for tools to find structure from chemical name.

I plan to use your programs to organize substances and reactions for my every-day lab-work.

Interested in calculating parameters such as log(P) for modelling the potential effects of complex environmental mxitures on human health

The FMP is an academic research Institute for Molecular Pharmacology. The software will be evaluated for use with an internal Web server for easy database access.

Nemours Biomedical Research is a not-for-profit organization dedicated to improving the lives of children through research.

The software will be used on the organic course website for the purpose of drawing and analyzing organic structures and reactions in support of basic organic chemistry education.

for development

Implementation within a LIMS System for documentation and quality evaluation in scientific research.

Student tasks in 3D modeling protein ligand intereactions. Methods: molecular dynamics simulation and e.t.c.

Water cluster analysis

Drug Molecule Characterization

management of a virtual screening database; QSAR studies of potential HIV protease inhibitors

Visualisation and generation of ligand conformers in computational chemistry

I want to use the software for generation of a compound library for some GPCR receptors. I am interested in generation of 3d conformations from given SMILES notations. Later I want to use these conformations for similarity based grid searching. Your tool is very advanced for batch processing and library design.

I am working on the ceramic fiber. I want to use this program to prepare stucture of my system.

determination of parameters for molecular dynamics simulations for academic research

Students are learning to work with modelling and retrieving of all kinds of chemical information. We work with a group of 50 students each year. No written implementation sofar

I am a new staff in my university,I want to use some softwares about chemistry to teach the student,if we find it useful ,we will feedback to you

we are studing the follows: (3 big areas) 1- K chanels in proteins 2- organics compound-metal surfaces interactions 3- material science we have a little centerof bio and cheminformatics and teaching this tools in bioinformatics engineering.

We are developing methods for the rational design of drugs that are robust with respect to drug resistance. Part of this research is a large virtual screen of potential HIV-1 protease inhibitors using AutoDock, our molecular docking software. I am evaluating JChem Base as an interface to our (PostgreSQL) data base of docking results. I may also look at some of the cheminformatics tools to support our ligand preparation and docking analysis activities.

Our research is on developing machine learning methods for virtual screening and for clustering chemical compounds.

To predict outcome of Organic reactions that I am investigating in order to make it more predictable and better.

creating 3D representations of molecules that are used in the lesson and exploiting some fonctionnalities of the program to illustrate and to study thoroughly the notion of pKa, the notion of resonance, the elementar analysis etc. completing the utilisation of plastic models to show the diverses sorts of representation of a molecule. the program would be used with a beamer in front of the class and at home to create a new course material.

We are building a webfront gui for CHARMM, We would like to use marvin space for viewing the structures of the generated PDB files and to generate the surfaces for the PDB Files.

to selecte some pollutants in the ground water and draw some of them. I’ll use it just for me only to see the molecule. It could be then easier to speak about.

Using to draw structures for my online lecture notes.

JChem will be used to virtually screen for SUMO inhibitors.

Molecular modelling of a number of new heterocyclic moities are undertaken with the aim of finding new molecules for effective treatment of AIDS, TB, cancer.

Use by my organic chemistry students

Modelling p450 2e1 and its active site

organic chemistry

physico-chemical descriptors of anti-HIV drugs.

I intend to use this application for analysis of some herbicide class characteristics

mcs search for finding new scaffolds for combi-libs

I WILL USE THIS AS AN ADDITIONAL TOOL IN MY TEACHING

Faculty of Pharmacy has launched recently a PhD programme in Drug discovery and medicinal chemistry, thus it will very useful to have your software for training our students.

Marvin and Jchem will be use in our screeing center to enable students to evaluate avalble compounds and librarys. As well as durring the creation of new compounds.

The aim is to introduce the in-silico technologies implemented in the fields of virtual screening and structure-based drug discovery. In research, I focus on facilitate technology for probing hot-area and extracting biomolecule-compound interaction pattern.

evaluate product to be used in ochem

rational drug design

Teaching biochemistry classes – Illustrating lecture slides Research: peptide display and structure-fucniton exploration

Study the physical properties of organometalic complexes and of metal nanoparticles.

The calculations plugins and MarvinSketch will be used to generate models for syntheses, experiments, and collaborative purposes. Structures generated in MarvinSketch will be used to help facilitate understanding of key mechanisms. The conformations tool will be used frequently to find the lowest-energy conformation of an organic molecule.

Research: We are a research group working in the fields of Cheminformatics and Chemometrics. Current projects include Virtual Screening (mostly antivirals), QSAR (various targets) and ADME/TOX predictions. MarvinSketch will be used to draw chemical structures for export to mol2 which is used as input for several software and for the production of chemical figures on posters and publications. The database features of the package will most probably also be employed. Teaching: We hold courses in computational chemistry, where students rely on a program to draw chemical structures. Furthermore we will use MarvinSketch to draw figures for presentations in lectures.

Test of chemaxon tools to develop a web docking tool.

we are attempting to find brain imagiong agents. evaluation of pka, logd etc are importantb issues for these agents

Freshwater contamination from microbiological and chemical contamination poses public health risks. Chlorination has been the most commonly used technology to eliminate microbes in drinking water. However, chlorine reacts with traces of DOM in water to produce disinfections byproducts (DBPs) that are carcinogenic and tumorgenic to test animals and the ones being regulated by law are THMs and HAAs. Modeling is the only option for predicting the formation of DBPs. Linear and non-linear models, which related chlorine consumption and water quality parameters are commonly used. However, this approach has three drawbacks: it requires measuring water quality parameters that is tedious and time consuming process, .the model developed is not robust as water quality change with time and space and finally it disregards the molecular features of compounds that react with chlorine. This research focuses on Quantitative Structure-Activity Relationships (QSAR) as alternative method to other models. QSARs are used to predict behavior of molecules based on their chemical structures. It makes use of structural features of molecules as descriptors to produce a set of possible equations. Some of the features that can influence the reactivity molecules in water are acidity (pKa), hydrophobicity (logP), logD), polarizability, isoelectric point (pI), Charge distribution, orbital electronegativity, resonance, typology, etc. These descriptors are assigned numeric values using special software such Calculator plugins and are related to chlorine consumed or DBPs formed. The model compounds that will be used in development and calibration of QSARs include aromatic compounds, aliphatic compounds and amino acids. Where no sufficient data exists, bench scale experiments will be performed to supplement the database. The performance of QSARs will be tested using published humic acid and fulvic acid model structure and compared to empirical results available in the database.

I am interested in chemioinformatics and drug desining.

Using all the ChemAxon tools to visualize, transform store, and search compounds and reactions. Developing a specific similarity search on reaction, including some sort of selectivity search. I would like to merge my development with the ChemAxon tools, by using the ChemAxon API supplied.

calculation of physico-chemical properties of compounds. chemoinformacs

If apprpriate, the software will be used in teaching to make calcuations of chemical properties related to the environmental fate and effects of organic chemicals. The purpose of the course is to teach how structure-activity relationships can be used for environmental management purposes. For research purposes the software will be used to make chemical proerty calcuations for chemicals to explore structure-fate relationships of organic chemicals.

i am a student studying chemistry at anu

would like to demonstrate orbital interactions, esp for organic chem; electrostatic maps for org, gen, and biochem; protein folding in biochem; host ligand interactions for org and biochem want to try for evaluation purposes first

Determine microspecies of drugs for complexation to polymers.

Teaching – demonstrating the use of toolkits and web-enabled chemical informatics software in both an introductory chemoinformatics and programming for chemoinformatics class. Research – processing and visualizing large chemical datasets, demonstrating use of web service workflows for HTS analysis and other drug discovery processes Publications in preparation

For use with AP chemistry and drawing organic structures

Cheminformatics Database Construction

JChem is interesting for us as it will help us to regularly update our in-house databese that merges commercial supplier databases used for virtual screening. Marvin is used to draw and view structures under other platforms than Windows. The other products will be discovered my our lab members and if they like the package they may use some tools for teaching purposes.

physico-chemical properties of drugs characterisation of drugs correlation-studies

synthesis

I would like to use the Marvin software for creating 2D and 3D molecular structure for an organic chemistry course. I am also interested in calculating solvent accessible surface areas with the calculator plugin for research on the dissolution of organic crystals.

I will primarily use the softwares provides to pridict unknown chemical information for some pharmaceutical compounds that are used in our research.

Creating teaching resources Use for students

The JChem package will be very usefull to my tesi work expecially for the structure canonicalization feature involved in the docking and massive virtual screening process. My tesi work deals with implementation for a ligand-protein docking program to treat the desolvation model in a more realistic manner and treat the flexibility of the protein active site side chains.

Determination of structure new complex compounds containing Copper (II), phen, bpy, dicyanamide and a a free anion, need for theoretical calculations

I am a PhD student and my research work is about some ligands and their ability to coordinate some metal ions like Cu(I), Cu(II) and Zn(II). I would like to study their ability to cross membranes.

I teach chemistry courses, including organic chemistry, and biochemistry courses. In additon, I am engaged in research exploring the mechanisms of drug resistance in HIV reverse transcriptase. This work, and the work in the classroom involves the extensive use of images of molecular structure (from large proteins to small organic molecules). We use structure to explore structure-activity relationships, drug design and chemical reactivity and mechanism. To have a comprehensive suite of drawing a viewing programs that can facilitate this teaching and research component is very attractive.

Teaching molecular modelling, inorganic and organometallic chemistry.

For use in visualizing, minimizing and searching molecules relevant to UsefulChem, an Open Source, Open Notebook Science project. The project is currently mainly involved with the synthesis of anti-malarial agents. Students working in the lab need to access the molecular information. Students in class write about how what they are learning is applied in real research.

I run a website called MolecularMagic for public and for the students I teach Chemistry to at my School – Eaton Bank School, Congleton, UK. The site currently contains a molecular structure viewer which is based on chime, moodle and a concept map server. I would love to integrate Marvin sketch and associated applications into the main site to allow my students, and anyone else who visits the site to construct diagrams to include in writeups and reports. I intend to customise the appearance of the applet a bit in the near future, but wanted to make it available as soon as possible. To view what I’ve done, visit http://www.molecularmagic.net, hover over the title and select ‘marvin’ from the menu.

I am Assistant Professor at the Istanbul University, Department of Chemical Engineering. I want to use this programm as teaching purposes in my underground classes. I thank you for your interest.

I am interested for a first part in the description of the protonation state and the conformational state of chemical compounds at particular pH value and for a second part, I will use these compounds to experiment new molecular descriptors

peptide chemistry/biology

I would like to use the tools in my lab and in the classroom. The main use will be research, which is described below. However, I would also like to use the tools in my graduate class, Med Chem 534. I teach a section about online tools for cheminformatics. No presentation would be complete without covering ChemAxon’s presence on the web. A large focus of my group’s research is in structure-based drug design. We plan to use the ChemAxon suite of tools in the preparation of our small-molecule virtual screening libraries. Standardizer will be used in the canonicalization of the small-molecule structures. Calculator Plugins and JChem Base will be used for the selection of “lead-like” compounds. My group also collaborates with experimentalists doing High Throughput Screening (HTS). We would like to use the Marvin tools for the visualization of HTS results and selection of hits. Hits identified either through HTS or virtual screening may be expanded on using the Screen, Reactor, or Fragmenter tools to search existing compound libraries or create new virtual libraries.

Undergraduate and Master students will be trained in this software as important tool for chemical sketching, compound and proteins visualization as well as QSAR descriptors calculation which are important tools in drug discovery today.

For some web display, but mostly as a structure drawing package for students.

I’m studing computer aided molecular design . THe research theme is transdermal skin penetration usign enhancers. I need to calculate logD at pH 5.0~6.5

The softwares you are providing will be nery useful in concluding structural and functional properties of drugs, what we are actually dealing with. So using these softwares would be an advantage for us for the research we are proceeding with..

I have a particular problem which implies the calculation of the pKa of different molecules and would like to try the Marvin ability to do the job. Besides, we are considering the installation of ChemInventory which uses ChemAxon products.

These programs will be utilized to advance the pharmacologic research taking place within the core facility. Many novel pharmaceuticals are evaluated with little knowledge of them. Characteristics such as solubility and pKa and very important and will be clear uses of the software. This will also be a tool for educational purposes as there are students who make their way into the laboratory envirnoment for individual projects and/or are enrolled in the cancer biology program at the University of South Florida. These tools will be vital in both aspects of research and teaching here at Moffitt within the Core that focus on clinical pharmacology and drug concentration determination.

the pKa and solubility tools will be used to elucidate the important chracteristics of pharmaceutical compounds to aid in the development of assays for detecting of theseanti-cancer drugs in biological matrices through liquid chromatography and mass spectromentry. In addition, our lab contributes to the cancer biology graduate level course by teaching sample preparation techniques, liquid chromatography/mass spectrometry use, and basic pharmacokinetic calculations. The software will be a great asset to our teaching and research.

My research is directed at molecular modeling and design of imaging agents. We currently work on a variety of platforms, Linux, Windows, Mac and Irix and I’m looking to standardize on software that can run on all platforms. We do modeling; protein and small molecule with a particular emphasis on metallic coordination complexes, QSAR, and docking studies as well. Currently I’m most interested in developing virtual screening techniques for imaging agents, and am looking at developing a database solution capable of handling unusual coordination complexes.

Antiviral drug development and discovery

We areintersested in Structural and Biochemical studies of Proteins and RNA., and in Structure based drug design studies of interesting targets.

I would like to utilize these programs to allow students to interact with molecules via the computer: students would be able to build and investigate chemistry using technology they are already familiar with. The programs would enable me as the professor to create interactive homework and/or laboratory assignments in an innovative way. Our institution in focusing more and more on the integration of technology into our core classes. Chemistry is continually on the cusp of new technological advances, and I would like to expand our program with the wonderful opportunities this software would offer me.

i would like to search for substructure of two smile strings.

We will use this software for carrying out projects to MSc MPhil and PHD students of Physics and Chemistry apart from Bio Chemistry Students. For teaching MSc we would conduct seminars on special topics and carry them over to other 12 colleges that come under RUSAC (Rural Society for the Advancement of Chemistry). Ours is a RURAL college admitting students irrespective of caste color or creed. The College is accredited by A grade by NAAC (UGC, Govt of India) and is affiliated to University of Madras and Thiruvalluvar university. It was established in 1922. We would update all our works to you.

Teaching : To understand how molecular properties are characteristic of the species they possess Research: Demonstrate the applications of molecular property predictions for chromatographicc separation predictions

Access to sdf files

drawing molecules, evaluate molecular properties, simulate nmr spectra, practice iupac nomenclature, ecc

For research purposes, interesting in using the package as part of my inhibitor design work. For teaching, interested in using aspects of the calculator in teaching about ionisation, biological bufferes etc.

RESEARCH DIRECTED TOWARDS FINDING ACTIVE CONFORMATIONS OF PHARMACOLOGICALLY USEFUL PEPTIDOPMIMETICS

Structural Biology (Structural studies of Protein-ligand/protein-DNA by NMR) Structure guided ligand screening

The aim of the use is to give molecules to student in a class, or for student when they take the class on PC.

i’m studying the molecular aspect of new HIV target drug. i’ll use this software package to characterize the structural aspect of hiv target drug. i’m focused on structural enzymology. so i need to know something about structure activity relationship of the molecules i’m linked to. this software package will also help me to make some features of interesting molecules such as medecine for the students i’m responsible of….

e-lerning, quantum chemical research

laboratory report, project report and presentation tool

Food Science, Food chemistry and Food Technologies. Protein and peptide, polyphenol and other organic molecules characterization by mass spectrometry

chemical discovery in biological network

At the moment I’m student of chemistry and I’ like to use the softwarepackage for my studies.

To show chemical and biological compounds for students use. This will placed on a web page format and put onto lab machines. Later it will be placed onto a web site to be referred to for students studies.

protein crystallography

chemical inventory

I intend to include the similarity and clustering tools in the final selection stage of virtual screening projects

drug design, chemometrics

molecular modelling techniques database creating and mining

Main interset is in prediction of pKa of organic molecules, to use with Capillary Electrophoresis research. Also would like to predict other molecular properties to investigate predictive ability of electrophoretic mobilities. In teaching owuld like to use predictions with student classes in introducing molecular modelling.

The software will be used to help develop synthetic protocols for preparing and purifying novel compounds to be used as metabolic labels for proteomic studies. Will also use the software to predict physical properites to produce compounds that are stable at physiological conditions

I am planning to use this software for some QSAR studies

through use this software during my postdoc training in Canada, I think it is very powerful. Now I just back to China, and start a new group in Shanghai institute of materia medica, China. (www.simm.ac.cn) I would be very appreciated if you could provide a academic license for me. Thanks so much! The software will be use to build a public web-access sever for academic world. It will be enable a small molecule database searching, format conversion, simple descriptor calculation, etc.

This software will be used to aid the understanding of those whom I am tutoring. The Marvin applications are superb examples of chemistry applications at their finest. The plugins, which only make the applications better, are crucial to the understanding of those I teach in terms of polarity, electronegativity, and pKa.

will be used for qsar research

creating worksheets, creating online courses with moodle (future use)

We are developing a database of small metabolites for teaching and academic research. This freely-available database contains detailed information about small chemical compounds of biological interest. We plant to use Marvin to show the interactive picture of the molecular structure.

I’d like to use and evaluate the products of ChemAxon.

Drawing molecules for insertion in teaching laboratory materials and chemical safety materials.

We are deveoping methods for chemical warfare agent analysis. At the same time we are conducting training courses for chemists from developing countries.

As I have to identify plenty of molecules by using LC/MSn, it would be great to access a software that helps me to present my results. Thus I’m very interested in modules related with chemical structures drawing and Mass spaectrometry Fragmentation.

We are having chemiinformatics and bioinformatics course at our department as a part of B.Tech biotechnology program. The program will be used to generate chemical structures of academic intrest like to show the structure of various pharmaceutical compounds. The program will also be used by the students to do miniprojects on bioinformatics involving chemiinformatics aspects like ligand-receptor binding.

I am doing QSAR study and wants to seperate the compounds into large groups based on the charge, i.e, anions, cations, zwitters or neutral. So I have to get pKa information especially the staus of compounds under physiological condition (pH 7.4).

The software will be used to introduce concepts of chemistry and to explore and model the relationships of chemical structure to chemical property.

Structural Biology

for making structure and their analysis.

Use of the software in method development. Visualization of chemical reactions, p.e.: fluorescence products. Main field of work is analytical method development within the clinical environment of university hospital.

WE are studying the structure and performance of the photosynthetic reaction centre in the bacterium Rhodobacter Sphaeroides, which may be seen at PDB.org, 2RCR.

I am teaching of several physical chemistry cources includeing molecular modelling and quantum chemistry. Our research has focused on ab initio molecular dynamics and surface reactions.

show molecular structure to students

drawing ligands for docking processes using the MD module of the tool

research : understanding mechanisms of ionization in electrospray mass spectrometry. For these scopes it is important to know some chemical-physical characteristics of analyzed molecules (pKa, LogP, charge, ecc..)

Screen compound libraries for aquisition

Virtual screening pipeline course in JAVA for Bioinformatics Master

Evaluation of lead hits generated from our high-throughput screening facility here on campus in an effort to relate inherent or calculated physical data (clogP, PSA, etc) to QSAR analysis.

I work on biochemistry of neutrophils and discovery of immunomodulatory compounds.

To draw and evaluation structures of chemical compounds

For personal education to explore posibilities of modeling chemical systems.

To be used in our structure based enzyme inhibitor design research programmes

Schoolteachers training

Teaching Physical Chemistry at undergraduate and graduate level

Middle School Physics classes.

People can draw a molecule and post it into the forum if the need it to ask a question or for the answer.

The software will be used in Chemical Biology Research to determine the role of aspartic protease enzymes in the immune response. We require 3D viewing of biomacromolecules as well as computational utilities for calculating proerties fo small ligand molecules and inhibitors.

I have a small acdemic lab and I am interested in antimalarial drug design.

I’m a student and I need software to draw chemical reactions for papers and reports.

Will be used during an internship to obtain a masters degree in BioPharmaceutical Sciences

Molecular design of functional materials (organic materials)

Forensic Science purposes

prediction of lodP of newly synthesized organo-germanium compounds

Illustrating biological structures and their components (carbohydrates, lipids, nucleic acids peptides & proteins) largely for first and second year students.

we will try to compare virtual screening with in vitro and in vivo results.

I’d like to evaluate this software for teaching students in my courses to draw/visualization of medium size organic molecules. We use GAMESS for computing and need some tools for input files creating.

diferent courses in organic chemistry

Initially, it will be evaluated as a drawing tool and properties prediction for a few cases; if the tools are used for preparation of publications, it will be acknowledged and this description wil be updated.

Software will be used to draw chemical compounds for courses in general chemistry and organic chemistry.

provide user access little compound databases for drug design research via wed-based interface

General Purposes

My research is in bioinorganic chemistry. We will use the programs to calculate log P, log D, polarizability,draw structures, and …

pKa, boiling point, meltin point, magnetic susceptibility, dipole monent, dielectric constant

We are developing A Portal of an Integrated Molecular Stucture Database of Antimicrobial Components from Natural Resources. Our objectives are 1) To develop an integrated database for molecular structure of active antimicrobial components, 2)To compare the molecular structure of isolated antimicrobial components in the integrated database in order to determine similarities/differences of the components and 3) To provide a visual query interface and user-friendly query language for facilitating the interaction of scientist with antimicrobial component databases. We plan to use Chemaxon products for this research as follows: 1) Marvin Sketch to allow portal user to draw the structure of any component for similarity search. 2) JChem Base to be used in our integrated database. To date, no accessible online implementation is available. We are just starting this research, thus future change on the use of Chemaxon products will be notified.

Student Use only

I’ll use the MarvinSketch as a useful tool in the chemical, biochemical research. use its mol file converter, use its calculator to predict the theoretical properties of some chemcial molecules.

I am intending to evaluate the drawing package as a means of generting 3-D structures for modelling.

I will teach library design, pharmacophore search, clustering virtual HTS. For accessing the web implementation I will need to obtain an URL first. When this is available I will provide this information

I will use this software to calculate pKa and logP values of API’s to develop new formulation strategies. Also the 3D geometry calculation of those compounds is important in this area.

The package will be used to input molecules, then pass the corresponding SMILES code to a homemade software designed for creating graph machines. These are structured neural networks used for QSPR/QSAR studies without computing any descriptors. Third year ESPCI students should work on this project.

Plant metabolic profiling

I am involved in Structure based design and QSAR. I will be in very much need of the descriptors for my research. I have used your ClogP and PSA online and found it very useful

For grapical display of structures, database screening and property calculation

This software will be very usefull on ligands like phosphine and amines pka’s evaluations. Also, it will give a hand on calculating the electronic donor or withdrawng effects of differents groups attached.

I am an undergraduate learning about partition in particular logP calculations for completing assignments and coursework. I help in a research group during the holidays and may evaluate using JChem as an alternative solution for maintaining the in-house chemical database.

We are doing some SAR by NMR and this suite of programs will be helpful in managing our fragment libraries.

Calculating pKa and logD for drug like molecules.

Teaching drug design, cheminformatics Library construction for virtual screening efforts in cooperation with the School of Pharmacy.

I am doing a PhD in Organic Chemistry. Particularly I’m working in the development of New Methodologies for Peptide synthesis. In my field it would be very interesting to have a software that predicts pka values

I need ChemAxon sofware now for studying but later on it would be a helping hand in doing research and composing reports. The thing I would need most is MarvinSketch for 2D molecule modelling (that program has a wonderful opportunity to save sketches with .jpg file extension so that I can import those .jpg-s to the text editor).

Demonstrating sructures during the lessons with beamer. Drawing structures for work sheets or tests.

This software will be used for various teaching purposes and to assist graduate students and lab assistants in the teaching of undergraduate and high school students currently working in the lab. Also, this software will be used for creating presentation for teaching purposes and in the hopes of future implementation into an academic class setting.

Drug Design (Chem 162B) with focus on computational methods. We discuss ligand based drug and target based approaches and do short tutorials with some software.

We are interested in machine learning algorithms for QSAR and evaluating systems for computing descriptors.

We have compiled a database of enzyme-catalyzed reactions categorized only by the functional groups that are transformed in the reactions. The database is intended to facilitate the search for enzymes capable of performing desired reactions, either in isolation or as part of novel biosynthetic pathways. The ChemAxon software is to be used for viewing the substrate and product functional groups that appear in the database. This database will be used for research, as well as for pathway design projects in courses. We expect to make the database publicly available via the WorldWideWeb.

Use of computer chemistry modeling to help in understanding of bonding, chemical reactions, and appreciation of the 3 dimensional nature of molecules.

I use the software for the research on the profiles of natural products,including chemical-physical properties.

I am studying metabolomics, and have found this package very useful for looking at the structures of molecules that we are able to identify. Isomers and conformers, especially of sugar molecules, can be difficult to imagine in a 3-dimensional view without being able to rotate the molecular image.

I am interested in Developing A Molecule For my Research Work on p-53 .

I am professor of Quantum chemistry and Physical chemistry here in Cartagena University. Our work is focus in calculation of quantum chemistry and we are using programs such as Gaussian, Gamess, Hipechem, spartam, Molden, Sybyl.

I will be using the software in Prof. Lee Rubin’s screening laboratory in the Harvard Stem Cell Institute.

Identifying and modifying of known or novel natural product from fungi.

Design of drugs for neurodegenirative diseases Chemical Properties Prediction

We wish to integrate an inward and outward-facing searchable cheminformatics database containing novel chemical descriptors of datasets with hooks to group PLS/KPLS/SVM modeling. Our aim is to incorporate and utilize group best practices to validate and make known the applicability of QSAR to molecular informatics problems. Our efforts will be publicly accessible with the MLI, as a part of NIH Exploratory Centers for Cheminformatics Research funding.

I’m interested in potentially implementing/developing tools that could be used in on-line/distance learning courses.

Chemical Physics properties calculations, file format conversion, building Molecules under Linux OS, Drug Design studies

Mathematical Modeling based on molecular descriptors and QSAR development. Study of the structure of drug derivatives and theoretical analysis of the compounds.

Draw molecules for working and publication.

I came across MarvinSketch through ACEOrganic for my Organic Chemistry class. Compared to the other products that I have used in the past, this one is the best. I am also trying out other products which have been provided. I will also recommend these products to my classmates.

Implement small-molecule similarity and diversity functions when choosing substrate sets for GST and CYP drug metabolism studies.

Our center has been working on the drug design and discovery. We are very interested in ChemAxon, which has excellent performance in lots of papers. So we want to apply to academic licenses for using it in molecular modeling and lead finding.

I want to include it as part of an online course for non-science students. I have developed a Java template for drawing 2D molecular models (atom spheres, ball and stick models, Lewis strucures). Need to provide 3D renderings. Anticipate other members of the department will use it also. Presently developing applications on my university web page – will move to chemistry department page later.

i am interested in using the software as an aid during my course of study to visualise the structural molecules.

Simply, I am an eager undergraduate Chemistry student that hopes to utilize Chemaxon’s products to further my education.

Molecular visualization as a tool for computational chemistry studies regarding the protein folding problem.

I carry out quantum chemistry and molecular dynamics calculations of free radicals in condensed media and need a suitable tool to visualize the processes and products. At present my intentions are to produce graphics for seminars and publications. I have not given any thought to web based presentation of results. I recognize that if I present web based results in the future I will need to enlarge the scope of this license. (Please note: while I was filling the registration form, I hit return while aiming for shift and the registration was submitted incomplete. I think the missing information appears on this application form.)

I intend to model molecular monolayers on crystalline silicon to determine bond lengths and aid in the way I present the material to other researchers. Teaching chemical processes to non-chemists requires good tools and visuals that this package provides.

I am using these tools for organising lecture notes from classes I am taking at the university level and writing papers for credit in these courses

Research in Macromolecular Crystallography

Study of gold nanoparticles in particular synthesis of ligands and electrochemical properties

INTRODUCTORY COURSES ON MOLECULAR BIOLOGY AND MOLECULAR EVOLUTION. ALSO MEDICAL HUMAN GENETICS. RESEARCH ON LEAD COMPOUNDS BASED ON QSAR.

We need a chemical inventory software solution to manage all of our chemicals for the general and organic chemistry laboratory programs.

As a student in a drug design class, this program will be used for the topological analysis of compounds in determining QSAR for selected systems.

Estimate solubility, molar mass, MS fragmentation

I would use this software for graduation and then for biomolecular research. (I hope ;P)

we are doing medicinal chemistry and are currently investigating the utility of cyclic peptides as drug molecules. For these we calculate the 3D structures of the pepties and estimate their various physicochemical properties. One of these properties is the polar surface area. Using the package of this software we would be able to estimate correctly the 3D PSA. which is a very useful property for a molecule to have drug likeliness property.

for teaching purposes, it can be used to teach students of the molecular modeling course to manipolate and study the 3D structures of small organic molecules toghether with the 3D structures of proteins and other macromolecules. For research it can be used for creating good 3D publishing images and maybe other aspects that I can’t now immagine since I don’t know all the potentiality of the software.

I plan to start using ACE Organic for my organic I and II semester sequences and MarvinSketch is the main component of this tuorial system, so I wish to become very familar with this program. Also, I have an internet nursing majors class to put together and I wish to see how user friendly MarvinSketch might be for a non-majors class which currently does not have access to a drawing package.

I am a Chemistry/Pre-Pharmacy student. I will be using it for research to help enter the College of Pharmacy.

For use in drawing structures and for practice with ACE organic and/or OWL

Classification of small molecules according to their scaffold.

For the teaching of physicochemical profiling of drug candidates and QSAR approaches For research, used as key entry point for measurements of physicochemical properties of new chemical entities

In our laboratory are working on natural products of sponges from Canary Islands. Now, I’m writing my PhD Thesis so I have to draw a lot of molecules, in my introduction there are more than 140 molecules, from steroids to alkaloids. Moreover, the Calculator Plugins could be very useful in our research, especially those about Isomers and Conformation. In the references of my thesis ChemAxon will be cited, as well in any publication.

We would like to estimate if protonation proceeds or not for the combination of metallocenedicarboxylic acid and bis-pyridyl compounds. For example, we would like to estimate if protons of ruthenocene-dicarboxylic acid transfers to pyridyl nitrogens of 4,4′-dipyridylpropane.

I will use this software to visualize proteins in 3D, from PDB files, which will help me to decide which residues to mutate. For small ligands, I will try to use the hydrogen-acceptor, hydrogen-donor feature and other calculators, to think about chemical reactivity.

Organic Synthesis Asymmetric Synthesis Drug Discovery Quantum Caliculations

I am currenty modeling the molecular structures of a drug family. This will allow me to develop a Quantitative Structural Pharmacokinetic Relationship for the drug class

I would like to examine the possibility of incorporating your tools during the current semester (and the forthcoming summer) for use in Honors Organic Chemistry next Fall

Design small molecules analogs, for study in transport of protein transport Creatin

Would like to use the softwares to facilitate ongoing PhD research in our lab- mainly for QSAR studies and other chemoinformatics approaches.

I study volatile compounds of wine and their interaction with non volatile matrix and fining agents. I’m interesting in chemical properties of the compounds such as log P and volatility.

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Development of new ligands that block the aminoacyl-tRNA synthetase’s binding sites

Aplication of molecular descriptors in artemisinin derivatives

Drawing, rough estimate of parameters like Pka, logP etc, exploring some more benefits.

I plan to primarily use the software for creating pictures of molecules & reactions for exams, quizzes, homework problems, etc. in general chemistry and biochemistry courses.

I am a student taking organic chemistry lab and we are required to inclue drawn chemical structures in our submitted lab reports. I would like to use the program to accurately draw the structures for my lab reports.

Just to learn

To provide students with more access features and learning activities of 3D Chemical Structures in your applications package using for ACE-ORGANIC. To teach my students to take advantage of all the features in your Academic package Application. To help my students save time building molecular models by using your program.

I intend to use the program to obtain parameters for classical MD simulations I run with CHARMM

Use as a tool for drawing non-natural amino acids to be used in the contruction of generic anti-infective peptides for academic research (see e.g. my JID article 2006)

demostration 3D structure of certern proteins.

My main research interest is Raman spectroscopy and surface enhanced Raman spectroscopy. At present I am working on tautomeric molecules. This software will really help me to estimate the pKA value, the PROTONATION EFFECT of molecules, to estimate THE LOGP VALUE, MOLECULAR SURFACE AREa etc. I am using the gamess, gaussian, tinker software package and the outfiles of these software can be fed

Molecular Physical-Chemistry Molecular Spectroscopy Structural Analysis

Fabrication and characterization of organic thin-film transistors using newly developed organic semiconductors.

To include molecular structures in notes and presentations that will be used in lessons with the students – particularly A-Level.

The Small Molecule Discovery Center has a compound database of around 200,000 compounds available for screening. We have been using Pipeline Pilot in order to standardize and search through our collection, but we are interested in using the ChemAxon tools in order to make searching through the database more simple for our chemists and to have a more robust standardization system than the one we have been using.

Computational chemistry: Conformational search Optimization Fitting parameters

My research involves working with QSARs. The program will be used to convert mol files to smi files.

I would like to present for my student new molecule formats.

The software, will be used as part of the already developed software hk-means * *(J Chem Inf Model. 2005 Jul-Aug;45(4):807-15.). Additional use in other java projects is possible when the package seems to be usefull for the specific task within our group, but has to be evaluated by the individual group members when the need arises. hk-means will also be used in teaching where possible as part of courses about data clustering. If the packet components can be easily integraded into course project development, it will be used as a means to help our students to develop faster solutions for class assignments and allow them therefore to focus on the general theme of the task rather than waste time with trivial programming problems. If hk-means is used in courses, the package can/will be a part of the previousely named software.

I’m developing fragment-based screening methods against phosphatases. I’d like to explore ChemAxon toward the help design the libraries (using binning or similiarity searching).

Mi WILL RESUBMIT MY APPLICATION BECAUSE YOU TOLD ME SO BECAUSE i HAD PROBLEMS WITH LICENSE KEY FOR POLARIZABILITY. If THE PROBLEM CAN T BE SOLVED YOU CAN GIVE ME ANOTHER USERS WITH ANOTHERS LICENSE KEYS. tHANK YOU VERY MUCH, WITH RESPECT LACRAMA ANA-MARIA

I am currently exploring research areas for my dissertation that would benefit from using substructure similarity searching. The focus of my research deals with gene expression and whole genome scan data, but looking at chemical structures (and substructures) could provide a nice addition to my work (though not directly something I want to do research in).

I’m a young teacher and just started working with students in all fields of chemistry especially organic chemistry.

for use in organic chemistry 353 at the university of southern indiana. this software would be most useful in the furthering of one’s academic studies.

The software, will be used as part of the already developed software hk-means (J CHem Inf Model. 2005 Jul-Aug; 45(4) : 807-15.). Additional use in other java projects is possible when the package seems to be usefull for the specific task, but this has to be evaluated when the need arises.

Estimation of pKa values and standardization of metabolite structures for metabolomics and metabolic modeling purposes. No plans for inlcuding the products in publicly available tools.

The Optical Radiology Lab develops compounds used for targeted imaging of molecular processes. We need a system to keep track of our compounds, their properties, and studies carried out with them. Ideally, the database would reside on our lab server (running Mac OS 10.4, may be moving to Linux soon) and would be accessible by all of the group members through a web browser for adding and querying compound properties. Access will be restricted to members of our group.

Computational Chemistry e-Science Research

(1)Draw molecular structure. (2)Biochemical molecule(protein and DNA) visualisation. (3)Automatic Generation of 3D Molecular Structures. (4)Store the molecule structure in a library and can be find easyly. (5)Calculate the properties of the chemicals (like some amino acids).

development of practical sessions for undergraduates in computational chemistry

Research on in silico drugdesigning

Our Laboratory specializes in the synthesis and use of heteroatom based ligands in coordination chemistry and catalysis.. All aspects are investigated, be they fundamental or applied. We are mainly known for our research in phosphorus chemistry, field where we have acquired an important international reputation. We study transition metal complexes with different approaches: ligands design, study of ligand-metal interface (coordination chemistry), organometallic synthesis, homegeneous catalysis applications and theoretical chemistry.

Courses of general organic chemistry. Presentation matrials.

The software is intended to be used in the clustering and analysis of chemical structure databases. The work may result in the development of more robust and accurate algorithms for clustering of chemical structures. These software maybe used for comparison and other activioties like conversion of molecular formats, veiwing of molecular structures, measurement of similarity among structures, and etc.

Mainly interested in marvin sketch and marvin space as free alternatives to the costly ChemDraw and Chem3D. Also interested because I’m looking for a native 3D visualization tool that runs natively in OS X. Also interested in the conformations and calculations plug-ins we are finally trying to set-up a laboratory reagents database for our research group and are evaluating different options (ChemFinder, FileMaker)

Current interests lie mainly in the development of synthetic methods for surface-active polymers and amphiphiles, for their use in forming monomolecular adlayers.

I Like to use this software in a study.

We try to use the MCS functionality to solve the graph edit distance problem.

Structure-activity of drugs that are analgesics and antioxidants

Preparing chemical structures for teaching purposes (glucose, mannonse, xylose)

My interest is in dyes and stains used in biological and medical applications. I wish to develop an online database for chamical, structural and application/use of fluorescent and non-fluorescent chemicals. I am a member of the Biological Stain Commission and the Microscopy Society of America and have undertaken this as part of both my current job and my affiliations and interests. Finnaly, THANKS for the consideration. At the moment, I have nothing to add below.

I would like to use your poducts to build a chemical inventory system for my department.

visualization of the 3D structure of molecules; predicting properties like clogP, PSA, pKa

calculation of properties and descriptors. visualisation.

i am a student using this program to learn organic chemistry

I plan on studying green leaf volatilve compounds emitted from plants for my undergraduate thesis. I feel that the Marvin software will be invaluable to inform all aspects of chemical research.

Graduate research

I will use the software in course presentations to show the 3-dimensional nature of organic compounds. I will use the software also in research for calculating pKA’s.

Research focused on comparing sub-structure based screening methods with traditional fingerprints for chemial compounds.

I would like to use this software for prediction of pKa values for fluorescent pH indicators for optical biosensors. pKa values plays important rule in selection of suitable indicator. pKa values are not available for all these compounds and their prediction will save money and time for experimental determination.

Exploring the possible uses as it applies to molecular modeling using existing crystal structures

to draw and view molecules in word and powerpoint

Organic synthesis of non-natural amino acids

Generation of 2-methoxyestradiol conformers in order to test docking on alpha and beta tubulin dimers as well as calmodulin (folded and unfolded). Will aid in the elucidation of the mechanism of action in cell growth inhibition on cancerous and non-tumourigenic cell lines. (MCF-7 and MCF-12A)

The tool is going to be used for teaching purposes in an organic chemistry lab course for undergraduate students. This includes drawing of graphic formulae in lab reports.

USING FOR COLLECTION VARIOUS DRUG STRUCTURES

I visited the booth in Chicago ACS meeting and interesed in use the softwares for predicting properties of new compounds and new reaction in our group.

Molecular modelling

I am intersted in visaulizing the drugs usins software and to test the ionization at different pH, to determine the Absorbtion ,distribtuin metabolism and excretion.

Small molecule inhibitors of Mycobacterium tuberculosis, a medicinal chemistry approach which may be complimented by ChemAxon’s logP and Lipinski calculations. I would also like to introduce thise tools to other staff and faculty at ND.

to teach organic chemistry with database searching and molecular modeling stdies brieafly.

i want to use for filtering the databases based on lipinski’s rule

structural-function relation

I’ll be using this software to draw molecules for my organic chemistry class.

I am mainly interested in using the Marvin tools and plugins for use on Linux. These tools are far superior to any others I have found and I would like to take advantage of the more advanced features which require a license. The main use of these tools would be to produce presentation quality images of organic molecules.

The function of the program that will be used will be the pKa predictor tool. This will enable me to generate pKa values for organic compounds that I am working with and hence compare and discuss them. With successfully obtaining the license and being able to use the pKa predictor, I will reference the program in the PhD thesis.

yes

we are teaching MSC students using diffferent softwares

Because of possibility of single molecule detection, surface-enhanced Raman scattering is attractive. However relation between plasmonic nanostructure as SERS substrate and adorbed molecles are not well understood. Therefore, molecule modeification for improvement to ehnace the SERS are of interests. Additionally, thank you for excellent information at ACS booth.

I teach high school chemistry and chemistry of foods. Because the chemistry of foods class involves drawing many organic molecules, I am currently evaluating software that allows me to easily draw these molecules on the handouts I provide my students.

Environmental chemistry

I want to use marvin to calculate charges and other properties of small molecules

Downloading for use as part of a graduate class that involves examining small molecules interactions with proteins. May eventually use to examine possible interaction with synthesized compounds.

I am interested in using your software to manage my library of plant metabolites used for screening fungi for toxicity.

I hope to use Marvin for pKa and LogP calculations of my novel compounds synthesised as part of my PhD research project.

My research project is on Electronic and Structural Studies of the Role of Pyranopterin Dithiolate Ligand on the Enzymatic Catalysis of Molybdenum Containing Sulfite Oxidase (SO). We propose to determine how the pyranopterin dithiolene controls electron transfer reactivity and the modulation of redox potentials in new model systems for the pyranopterin molybdenum enzymes. This is proposed to occur via static or dynamic distortions about the dithiolene fold angle and/or via the redox non-innocence of the pyranopterin dithiolene ligand. The distortion varies with the occupation of the d orbital that is in the equatorial plane. We will explore whether pyranopterin ring opening might occur during the course of enzymatic catalysis in pyranopterin molybdenum enzymes. Ring opening of the pyranopterin can be thought of as a two-electron redox process on the ligand, and therefore should significantly pertub the electron structure of the metal site. The determination of dithiolene, dithione and dithiete resonance forms of the bound cofactor ligand to the overall electronic structure of the site will be a major goal of the proposed studies. The contributions of these ligand resonance forms may stabilize specific oxidation states of the enzymes during the course of enzymatic catalysis. In order to accomplish this research I need to calculate some molecular properties such as dihedral angles, bond length, charge distribution, orbital electronegativities etc which could be calculated using CALCULATOR plugin offered by chemAxon.

electron density visualization

Studying distribution of herbicides in soil

I will use it for corelating biological activty with molecular discreptors

Teaching for the postgraduate course Molecular Recognition. Research: Development of synthetic receptors based on rational design and combinatorial chemistry.

For teaching the students in Drawing, optimizing the chemical structures and calculating the properties of the molecules.

I teach analytical chemistry/instrumental analysis. I would like to use this program to help students understand the fundamentals of HPLC. The intent is to have students build a series of related organic molecules, have the program predict log P (or log D over a range of pH for ionizable molecules) and relate that to retention behavior. I am sure that other applications will follow from this success

We are working in the area of chemoinformatics of locally available medicinal plants.

Medicinal Chemistry Research – particularly on the fragment-based design of compounds using STD-NMR and X-ray crystallography. We would like to maintain a database of compounds, associated with biological activites and potentially X-ray crystal structures.

i would be using the tool for my database management and mining studies and teach the values to the student here.

carbohydrate engineering and application

Evaluation of tool set to support synthetic efforts

The main research topic is the study of polymorphism in pharmaceutical solids.

chemical structure standardization, fingerprint calculation, molecular similarity searching using fingerprints and MCS, local databases of chemical compounds.

Teaching

Drawing of different structures, 3D animation of molecules.

I wish to use the software to look at the physiochemical properties of drug and solvent molecules to investigate solvent effects on drug permeation through human skin. Examples of the sort of information used will be log P but also thesurface area of molecules, the molecular size and their ability to hydrogen bond. This will be used to form hypotheses of which solvents to include in formulations to enhance the permeation of certain types of drug molecules across human skin. This will be correltated with experimental results which will hopefully published in peer reviewed journals.

I hope than I can use your programm for research with hair dyes.

We are studying Ligand.

…

Organic Synthesis Bioorganic Chemistry Information technology Synthesis of small natural products see CV :http://www.arkat-usa.org/ARKIVOC/JOURNAL_CONTENT/manuscripts/2007/AK-1418GT%20as%20published%20mainmanuscript.pdf#search=%22krief%20Alain%22 Website: http://www.fundp.ac.be/facultes/sciences/departements/chimie/recherche/centres/cos/

The main purpose is to calculate the physicochemical properties of drug molecules to be used in modeling and simulations of in vitro liver cells.

Computer-based virtual screening promises the ability to screen millions of compounds rapidly and cheaply. Although virtual screening has long been the exclusive domain of computational chemists, a convergence of computa tional power, freely available software and large, high-quality databases of chemicals has ostensibly made virtual screening accessible to nonspecialists. I report a successful ligand-based virtual screen based on the Ca2+-mobilizing second messenger NAADP (nicotinic acid adenine dinucleotide phosphate) that revealed the most selective antagonist known. This antagonist, Ned-14, is structurally unrelated to NAADP and is fluorescent and drug-like, enabling it to block NAADP signalling and label NAADP receptors in intact cells. Further work is currently underway to find novel drug-like antagonist or agonist of cADPR, 8-amino cADPR and IP3. Additionally, I am using these computational tools to find novel inhibitor of neuraminidase for avian influenza. Recently reports have suggested (Nature 2007) that well-known neuraminidase inhibitor tamiflu has undesirable side effects and thus it is even more important to find novel drug like molecules to inhibit neuraminidase action.

QSAR/QSPR, dock

To perform conformational analysis on small molecules and odorants

I’d like to explore correlations between the QSAR of molecular interactions and the signals produced by capacitive, polymer coated arrays for vapor sensing.

I have used marvinbeans briefly as an undergrad at Brandeis University. I am currently doign research in DNA-protein interactions and am interested in seeing how Marvin can help me out

We are interested in screening ChemBridge small molecule libraries against kinase MAPKs. We would like to use your software for converting 2D sdf file to 3D structures, visualization and sharing with our colleagues on the epxerimental side.

learning basic principles of drug design

The physical chemistry courses for the chemistry, biology and pharmacy students are given in our institute. The program will be used for the demonstration as well as an application tool. our research is focused on thermodynamics of bimolecular interactions; including proteins, peptides, lipids and others. This program will offer us a priceless help in our work.

I will use in the Bioinformatics course. (teaching) In the research area we use for molecular modeling and to prepare the ligands for docking studies wiht proteins and DNA.

Our topics are: molecular biology, biochemistry, secondary meabolites, mtabolic pathways, focus is on plants, Arabidopsis, maize, cereales. Implementation: enzyme structures, comparison of structures, visulization of pathways and chemicl reactions for lectures and for publications.

I would like to use ChemAxon software for exploratory research with a medium-sized set of biologically active compounds, some of which I am testing in my animal models (metabolism / aging / oncology). I plan to create a small relational schema in mySQL that would support compound similarity queries. I will likely have custom analytical processes set up as scripts calling the database. I will also use the standardization / cleanup utilities, and probably clustering to explore the library. I will also maintain a local copy of the complete PubChem dataset.

Undergraduate learning. I have already had this software but have upgraded my laptop and would appreciate the licence details again. Many Thanks

To suppose the properties of compounds for new drug development

Software is to be used for prediction of pKa-values and LogD for various analytes of interest in my research.

Navigation system (browsing, retriving, archiving) of spectral data (NMR mostly, IR and MS), recorded at lab.

Computer Aided Drug Design: drawing molecules, property calculator, 3D conversion

We would initially like to evaluate JChem and Marvin as (a) standalone tools for molecular modelling and (b) tool-kits for integration of molecular structure and visualisation into web-based applications We intend to then add these tools to the curriculum we offer for bioinformatics software tools development.

In my PhD dissertation. To calculate logP, logD, pKa etc. for different molecules.

I am working with biodegradation of tannins and related molecules

protein visualization and partial charge analysis

Study of the optics and vision of extant artrhopods

We are currently evaluating many software packages for preparation of undergraduate labs in Pharmaceutical/Medicinal chemistry. The department also has many postgraduate students working in the field of QSAR and were interested in evaluating Marvin tools in order to build our in-house tools for research. We would be glad if you gave us this opportunity in using your reputable software package. Thanks and best regards, Ahmed

For a project of the subject Computed Assisted Drug Discovery.

HTS screening fatty acid uptake inhibitors

The focus of the research is to develop small molecules with the abilities to target specific biological macromolecules and achieve desired therpaeutic effects. An importanat aspect of this research is to develop compounds with desired formulatabilities and bioavailabilities. The software will assist us in predicting lipohilicities and water solubilities of the compounds.

I am starting the work on my PhD and I want to explore the possibilities that ChemAxon offers regarding conformational analysis and format conversion. As I have limited experience in the field, I hope that these tools will provide the help I need in dealing with structure analysis.

We are trying to identify fragments that might increase the activity in some of our assays. We tried couple of other programs for fragment generation and we want to try out your product too.

Cosmetic products technology. New raw material for cosmetic formulators

absortion of co2 in nanotubes, i make simulation

Organic synthesis.

Research aim to get logP values for potential drugs

- molecular modelling; - docking; - homology; - pharmacophore models; - virtual screening.

describing the metabolic pathway

I will be using marvin view to open sd files and then perform simple calculations on the molecules in the file. I am particularly interested in pKa prediction, polar surface area, cLogP, etc. I will also be evaluating these tools for potential use in a drug discovery course we are developing at UCSF.

I am interested in calculating refractivity of different moelcules to obtain the refractive index via Lorenz -Lorenz

We are handling the denovo designs of plant growth hormones.

qsar modelling,virtual screening

Using the software for three dimensional configuration of drugs in the pharmaceutical industry and new drug design

I am a second year graduate student working on the development of compounds to treat CNS Human African Sleeping Sickness. The Marvin software will be used mainly to calculate the physical properties of the compounds that are good candidates for the treatment of this disease.

Structures and interactions of protein and ligand complexes.

I am currently taking organic chemistry I at Clemson University, and am evaluating the tool to complete inclass assignments.

pestcine

Protein molecular visualization, crystallography of nuclear hormone receptors.

I’m a B.sc student for Chemistry in the mentioned instetued. I have came across your software and would have a use for it in the neer by future.

Teaching Module: in italian “Esercitazioni di Chimica Farmaceutica e Tossicologica” translation in english “Practices of Pharmaceutical Chemistry and Toxicology” an introduction to medicinal chemistry in the School of Pharmacy of University of Catania (Italy).

large scale metabolic models need the strong background in chemical compounds, which are used in model. We are developing Edinburgh Chemical ontology for unambiguous definition of compounds and relations between them.

I would like to use the software package to produce chemical drawings for use in my classroom presentations, as well as on tests, quizzes, and assignments. It will be used for first year High School Chemsitry, and AP Chemistry.

We are interested in the interaction of steroid receptors with ligand

I will use this software to demonstrate how differences between photosensitizers affects cellular targeting to visiting undergraduate students conducting research in our laboratory.

For understanding the structure activity relationship of cephalosporins and photosensitizers used in anti-microbial photodynamic therapy.

I would like to perform complete confornational analysis of previtamin D and it’s E-isomer, tachysterol. At least in gas-phase. I did not find yet if it’s possible to do it in solven, using your software. But for the beginning I need all the conformations within 3 kcal/mol.

I want to generate a fragment database using this software for de novo drug design.

I’ll use marvin sketch for pictures which will be included in report about a specific theme..!

Used for teaching an Introduction to Organic Chemistry and Biochemistry course.

Molecular modelling of MMP inhibitors in the active site

Postgraduate (MPhil, PhD) training for medicinal chemistry, where main focus is on the design and assay of new anti-cancer agents. Molecular similarity is used to assess likely prospect for new compounds – DNA, protein and lipid targeting. Biophysical assays are used to gauge behaviour of synthesised molecules. 3D methods based upon structure prediction with NMR and crystallographic structures.

Drug discovery

I´d like to use the software for calculation mainly of log P and pKa values to correlate the obtained results with another program entries and especially with experimental data as the part of QSAR studies.

peptide molecular dynamics simulations.

Teaching for molecular modelling, such as 3D-molecule build-up.

Generating pharmacophoric fingerprints to determine whether they can be used to develop interpretation software for surface mass spectrometry. Possible use in displaying chemical structure on the research group website.

i am a teacher of organic chemistry, when i give lectures about reaction mechanisms, i think some of the characters of the molecules will help student to understand it!

The tools will be used for collating analysing and for visualising the medicinal compounds as a part my phd research project.I am working in the area of bioinformatics and chemoinformatics.

We develop new stationary phases for chromatography. We need a software package that will allow us to calculate pKa values as well as logP and logD. Our aim is to develop a liquid chromatography phase that will mimic the shake-flask method of obtaining logP values.

This software will be evaluated for use in ongoing drug discovery projects at the CDD. In particular we are interested in the scaffold clustering tools that may be applicable to classifying large numbers of ligands that score highly in either virtual screening or similarity searches.

I am learning about the structure .so I am interesting with the soft.

I teach at the biochemistry laboratory in the food science department at the faculty of agriculture. I am looking for new methods to improve lecturing, and one way to do so is to use computer software in designing chemical formulas and molecules to be used in my presentations.

I intend to employ the software to develop research. The software will be employed in the first step of our research in order to determine all the conformers of a certain compound.

I research expert system for predicting toxicity. I need some different softwares for my research. Therefore, I want to have a trial version of this software. I look forward your reply.

teaching is good

Conductive polymer synthesis

Visualisation of compounds structure

To obtain a good medicine, I am retrieving various data bases though I want to make the thin film.

Calculating logD and pKa values

Organic Chemistry, mostly heterocyclic chemistry.

i need these softweres to get aid to my work

gcms applications

I am teaching general chemistry and analytical chemistry and I would like to use the latest in technology to help my students understand chemical concepts.

Software will be usded in the process of doing computer-assisted drug design.

Clustering, Reduction of redundance in structural diversity

Small molecule analysis support for mass spectrometry

I’m working on the molecular structure of natural organic matter in the ocean. The software helps to depict and develop possible structures.

organic synthesis, evalutaion of products from different route of synthesis

I will be using these tools to help with my chemistry classes, and research projects.

thsi software wll be shown it students who will attend in silico drug design programm in our institute.

We are working in computational chemistry, specially abot QSPR/QSAR, screening and clustering

The implementation involves teaching of chemoinfomatics using tools from CHEMAXON to undergraduate and graduate students, as well as research development of drug design methodologies.

Organic Chemistry students will use the software for modeling experiments. Students will work both on the bench and the computer to solve unknowns.

Calculating descriptors and making QSAR models

I have already generated a 160.000-structure database of ligands by means of LeapFrog/Sybyl and I need to predict some pharmacokinetics properties. I think some of these molecules are drug-like as antivirals.

I study Medicinal Chemistry

Structure based drug discovery to calculate the chemical parameters of the small molecules. Especially used for discussion of the inteaction between the ligands and receptors.

I am teaching Analytical Chemistry, Chromatography and Mass Spectrometry. I need your software for better chemistry calculations with my students.

The use of all modules is requested to use in drug design.

I am looking for new inhibitors of the Thymidylate synthase ThyX, a new therapeutic target recently validated by WHO for tuberculosis therapy, using screening of “natural compounds”.

Analysis of 3D files of compound libraries.

-teaching of students and graduate students from medical, chemical and nutrional science studies within our accademic hospital laboratory for diagnosis and research of nutrional and metabolic disease as well as within regular lessons of respective university curricula -research in the area of Metabolomics – LC-MS based analysis of metabolite concentrations in various body fluids (blood, urine, saliva, liquor…), multivariate statistical analysis, idenfication of unknown molecules, implementation and curation of databases of metabolites and methods

analytical chemistry

We investigate natural compounds as neuraminidase inhibitor of H5N1 influenca virus. We will use your software to investigate the substances ability for ligand binding to neuraminidase

studying the structure and function of G-protein couple receptor and their lignads

The Chemaxon package is suppose to implement in a part of my project work related to fragment based drug design.

My research group is interested in structure-based drug design. We use X-ray models of protein targets to guide a search for protein ligands. My students are working on a number of enzyme targets in their research projects.

molecular modelling, coordination chemistry

Biochemistry

data minig research for chemistry

we studied the CYP style of drugs. and i need to get the descriptors of these compunds.

Seeking to identify small molecules that inhibit viral entry into host cells. We will use the package to calculate pKa values of identified compounds.

virtual screening, docking, methodology development

We want to use ChemAxon tools for some chemical informatics applications : clustering and classification of inhibitors

Electroanalysis, electrochemical sensors

We are a crystallography lab that study protein glycosylation and I\’d like to use the software to model the glycans that we study.

Having been using chem suites on PC for six years, i\’m looking for a suite on Mac OsX – intel base PC. In our school we are working not only in classroom, but also with on line lessons for workers, and a graphic suite is really needed when teaching on-line chemistry.

I intend to use Marvin Beans to create chemical structures in Linux environment. Also plugins estimating pKa and LogP for molecules may be of use.

prediction of drugs used to block ion channel and structrue of ion channels

Cheminformatics project on new approaches to virtual screening. Project covers the quest for new drugs relying on many approaches, including computer-based virtual screening and docking. Over the past fifteen years, and in parallel with the exponential increase in the number of available high-resolution protein structures, many screening and docking methods and programs of use in the drug discovery process have emerged. The project aims to understand the similarities and differences of different methods as well as their capabilities and limitations.

Use to instruct myself further in how estimated chemical properties effect affinity and potency of compounds in pharmacological assays. My aim is to examine estimated pKa\’s of various opioids and assess any observed trends in values associated with pharmacological observed effects.

Solvation of organik nonpolar compounds on nonpolar solvent

We wish to use the MarvinSketch tool within the WebCT environment to assist students in passing questions and information among themselves and to the instructors. Our implementation may be based on the MarvinChat scripts, although we may find it more suitable to develop in-house scripts. We may also use MarvinSpace to present images in teaching materials presented through the WebCT system and/or via course web pages.

I work in analytical chemistry. I was looking for a good software able to calculate LogP and pKa. I will use Marvin for both teaching (in partical works) and research.

molecular modelling, dynamics calculations of variable linked to molecules,creation of database and use thereof and every other thing i can do with Chemaxon to make publication and help my institute

learning chemistry

possible activity corrolated to the pKa of ligands for the nicotinic acid receptor (wild type and mutated).

- computer-based drug design teaching

Courses: Geochemistry- water pollution Processes and Mechanisms. Research: Pharmaceutical contaminants within the aquatic environments using HPLC-MS/MS and SPE/LLE methods.

St. Mary\’s is a teacher training college. I am interested in showing student teachers the range of I.T. resources which can be used to enhance lessons. Also to allow lecturers to enhance their presentations to BEd classes.

Molecular dynamics calculations of the conformations of alkylarenes as influencing their infrared and nmr spectra

JChem will be used in a reasearch software system using evolutionary programming techniques aiming to the automatic detection of optimal ligands for protein docking. AutoDock will also be used. At present this is a brand new activity, in the context of a master theisis (Informatics Engineering).

Investigating the synthesis and design of fluorescence based sensors. Software will be used to obtain physical data for these molecules, e.g. pka, speciation, and etc.

I believe, that your software is perfectly applicable to show the students main aspects of medicinal chemistry and the employment of chemoinformatics. For instance with the pKa- and logP-plug-in. Students could experiment with the effect of structural variation on these values, which are important for drug devolpment. Also the pharmacophore related applications are interesting for students to get a better insight into medicinal chemistry.

trying to find pKa of M7, the major metabolite of Saquinavir for study of saquinavir metabolism

To teach undergraduates and graduates of chemistry. The implementation aims of this study are 1. to teach students about drawing and searching chemical structures. 2. If possible, use in molecular properties calculations. 3. Giving assignments and providing technical training all the chemaxon softwares with which the open access importance is realized.

One major goal of our introductory labs is to get students thinking about biological molecules as real entities with comprehensible properties. By presenting Marvin-generated images, I hope to communicate these ideas in concrete, memorable fashion.

The Tools should be used from the students to predict and see how pKa-values change, see the different conformations and chargedistribution of an molecule. They althoug shold learn to \”play\” with the 3D model of a molecule.

Want to do clustering and find representatives from each cluster using ChemAxon. This is for virtual screening.

Introduction to protein primary and secondary structure and post translational modifications. Aims: present amino acids and peptides three dimension form for presentation / teaching purposes. 1st year graduate level course. ~30 students.

To calculate pka,log d and log p values

I am working on organic chemistry

Draw Structure for paper, calculate 3D surface

The information provided from the programs offered in this site would be a wonderful tool to use for my Masters thesis in Chemistry. using these programs for pharmaceutical and biochemical research, I intend to pursue the effects of certain chemical structures in terms of metabolic pathways. hopefully these programs would offer a description or lead to information on a chemical\’s effects towards metabolic activity and biochemical reactions.

Teacing class of Biochemistry and research for biochemical compounds.

We will be using MarvinSpace in our Organic Chemistry lab program for students to draw and manipulate molecules. For example, we are doing a lab exercise in olfaction where students catagorize the smell of molecules based on size and polarity.

Calculations of pka and visualization in the preparation of molecules used in molecular docking experiments.

For anti-malaria compound design.

Development of NMR methods of molecular structure determination Determination of the 3D structure of organic molecules

Design of polymers and phosphorescent materials. Drawing of structures for publications

Solutions Chemistry: correlation between structure and pKa or log P Quantum Chemistry Introduction: application of molecular dynamics, etc on the prevision of macroscopic proprietes, etc. General Chemistry: structure design

EARTH is a non-profit international university where I teach Chemistry/Biochemistry to undergrad students of agronomical/environmental sciences from more than twenty countries -mainly from Latin America and the Caribbean, but also from Africa. Your software package will be very useful for the visualization of structures which will be conducive to a better understanding of the chemical/biochemical processes discussed in class.

Research will involve using the Topological feature to investigate molecular flexibility with respect to crystal packing.

I will be using this software for my PhD thesis, which involves the usage of different chemicals as postitvely or negatively charged molecules. The software will be mainly used to make sketches of the chemicals I am using in order to copy them in my thesis, as well as finding the isolelectric point of those chemicals.

I am interested in using ChemAxon to calculate pKa, logP, and logD values for some small molecules and use them as input in our models to predict intracellular accumulation of small molecules.

I will calculate logP, pKa, 2D and 3D surface area values of known and unknown drugs, used in pharmacotherapy.

I am working on a project of rational molecule designing to inhibit an enzyme involved in membrane dynamics. I plan to use this software for the molecular structure making, similarity search etc. Till now I have been using catalyst and cerius2 packages but people have recomended me to try these tools to have a comparative measure. I would be grateful for the licence.

For use in Chemistry Core Curriculum courses – Chemistry of Crime Scene Investigation and Molecular Architecture. Both course use molecular modeling as a module. Students need to draw and visualize chemical structures.

Implementation in undergraduate chemistry and biochemistry courses. Students would use the software to draw structures and to incorporate images into papers and lab reports.

For bioinformatics course to PhD students, We may or may not use it in research, depending on its capabilities.

Software used for drug designing project work for the students of biochemistry and biotechnology department for their M.Sc and M.Phil courses.

teaching: use it as versatile visualization tool

Needed for my class

Manipulation of molecular data for PhD purpose.

creazione di un database di molecole organiche

The product will mainly be used for structure guided drug discovery work. My group is working on targets related to cancer, tuberculosis and cardiovascular diseases. The work is collaborative in nature. My own lab is working on cancer, while tuberculosis and cardiovascular work will be in collaboration with my colleagues at the institute.

it is assigned to students as a study tool

We are developing an open access educational-academic drug discovery process for developing world diseases. We call it \”Distributed Drug Discovery\” (D3). We have demonstrated that through D3 students in Russia, Poland, Spain and the US can make potential drug molecules as an integral part of their education. A critical component of D3 is generating open access virtual libraries based on the simple chemistry these students can carry out with inexpensive equipment. The virtual libraries will then be analyzed with developing world disease computational models and the selected set of candidate molecules synthesized by our distributed network of students.

We are trying to convert the structure of a drug that we have been studying from 2D to a 3D format. We wish to model where this drug blocks the potassium channel that we study.

Analysis of small molecule HTS hits as they develop towards leads. Predominantly to use clustering of hits against library for SAR analysis.

Drawing of chemical structures for presentations and posters. Topic: Organic Synthesis of natural products isolated from tropical lianas.

I will be using the tools to teach chemistry to highschool students. I will use the tools in the classroom to encourage the use of chemistry in everyday life. I will use the tools to lead the students in exploration in the lab and inplementation out of the lab. I will use the tools to further the use of chemistry technology in and out of the school. I hope to encourage the interest of chemistry for all of my students.

The softwares would be used for teaching post graduate students at the deparment of life sciences, university of mumbai.

Intend to use cxcalc to generate multiple conformations for small drug like molecules.

virtual screening

Marvin will be used as my primary chemical drawing program on my MacBook. It will be used to generate recitation presentations, problem sets, and quizzes, as well as being used to introduce students to chemical structures in general.

Recognition in Supramolecular Chemistry

Chemical informatics for the compounds, chemical Database access,

Researching as an Organic Chemistry student.

I am a student and need this program suite for academic purposes.

Classroom teaching aide

Presently i am involved in teaching my students Physical Chemistry and Biophysics along with Medicinal CHemistry aspects and Drug design. I would like to see how far i can use these tools for better understanding of the computational methodologies.

Organic Chemistry 255

Computation and Chemistry

I will be demonstrating in undergraduate labs and supervising undergraduate students. I expect to use the software to introduce students to the concepts of chemical bonding, pKa prediction etc.

Research for residues of veterinary drugs and metabolites of them. Chromatographic and sample cleun-up methods are developed. Knowing the characteristics of these compounds gives the possibility of more efficient developement. Next to this the software will be used for personal education during my Masters.

I am working on several QSAR models to predict properties such as oral clearance and cytotoxicity from chemical structure.

I\’m going to use the software for study porposes and specifally polarity of molecules in three dimentional shapes

I use ACE for student practice exercises in Organic Chemistry. I have tried to use some features of ACE and have been denied access and want to be able to use all features. Thanks for you help

Calculation of structural properties, e.g. deprotonation state etc. and conformation of molecules in different environmental conditions.

Organic chemistry

generating data base and searching through, calculation of conformers, drawing and editing structures

Teach undergraduate students performing research to use modeling to accelerate research in synthetic methods and host-guest heme model compounds. Integrate into existing computational chemistry research for structure & geometry optimization and free energy binding for ion-porphyrin model systems.

Used for laboratory reports

DrugBank

I am a student who is currently enrolled in organic chemistry, and I would like to try this product simply because I find it more useful than your competitors (e.g. chemsketch).

Study for small molcule-protein interactions.

We are running Bioinformatics course. and planning to start Cheminformatics course

We are evaluating the use of chemicalinventory.org software for use in our stockroom. It interfaces with chemaxon It will be available to our student workers, staff, and faculty.

Property calculation of carbohydrate conjugates.

The research aims to explore structural basis of protein-inhibitor interaction by using our in-house database. The software would be useful to our understanding of small molecular inhibitors.

We would like to manage our data on small molecules and use it for the design of virtual libraries.

chemical database analyses, selection of the database

I am research assistant and I want to use that sotware in a research project. I intent to design a system that takes a equation and give the traditional name of the molecule. That\’s why I need a licence.

Allow the student to draw and manipulate structure, and run basic calculations on their molecules. The software will initially be used by upper level undergraduate students.

small chemical library generation and screening

mitosis

I am currently a student at brandon university. Because of my chemistry minor, i am needing the full use of your software in order for me to be able to compete lab reports with the upmost professionalism and simplicity. No other software package that i have used provides me with the tools that i need. Thank you ChemAxon.

visulization of 2D/3D structure, compound database management, structural similarity search

Organic chemistry of the PharmacyDegree and Postgraduate Pharmacy Studies

At the moment I\’m most interested in your fingerprinting procedures and molecular similarity and search calculations using graph matching. However, I\’m very interested in chemoinformatics in general and would like to get familiar with your software and its capabilities. I also have a student who need to perform some similarity calculations but she has little computational experience so would rather use existing software herself, instead of writing her own programs. The research is centred around the structures of metabolites found in human metabolic pathways.

I am developing a course on medicinal chemistry to be taught at Spelman University. We are evaluating this software to be used as part of the course.

I putting together a digest of bio and chemoinformatics tools with the purpose of course instruction. I believe ChemAxon offers a comprenhensice set of tools for the classroom. My focus is to enhance the learning and teaching experience through innovative technology. Marvinbeans fit perfectly the bill. In advance, I thank you for your time and consideration.

We use Marvin to graphically view and send data with our organic chemistry teacher. We have learned on this program, and use ACE Organic, which also uses this software. I\’m not sure if this is the licensing you had in mind, but Marvin is asking for a product key for several features that, while not required for class, would help me to have, primarily so I can see structures more clearly.

Mainly I am going to use the applets for the Chemical Inventory software to list all chemicals in stock and the places where to find them.

the students\’ ability to predict properties from the structures they draw is limited. I think the Marvin add-ins will help

Coal related

I am engaged in a program to target antioxidants to mitochondria. In this work, we synthesize targeted antioxidants and test their effectiveness.

We teach quantum chemistry and the students will use the software to store their results and make them available to others.

ACE Organic

drftgy

I am teaching molecular modeling at the master level. The teaching covers molecular modeling, force fields, MM and MD calculations, small molecule docking I am also involved in research projects concerning transcription factors (nuclear receptors and their partner proteins). I am more involved in ligand docking aspects, in silico ligand screening, and ligand design. I would like to use the chemaxon suite to handle the small molecule library, classify and extract the small molecule according to given properties.

I am an undergraduate biochemistry student involved in current university research. My chemistry education and research focuses on biochemistry, but my education in general covers a wide range of other chemistry topics. My research area is in the biochemistry of gastrointestinal stem cells and involves the study nucleic acids and various poorly understood proteins and their functions. Your tools would be useful in expanding my knowledge of the functions of such molecules related to my research. In addition, your tools would be also useful applied to my more general chemistry educatinal needs.

doing my homework

i intend to use this software in calculation of molecular descriptors specifically for QSPR and classification of anti-hiv ligands. as a student i don\’t have an institutional address but you can confirm it by mailing my adviser ssb@udct.org

It well help aid in teaching organic chemistry to introductory college students.

personal student use

benchmarking for small molecules database

Used to draw molecular fomulas for classroom presentation Models will not be placed on web site

Implementation of computational aspects of computer software for use in AP Chemistry and AP mathematics courses. Instruction of students in the use of software for computational chemistry.

Extension of laboratory work to private computer for study throughout coursework for class, Evolution of Protein Structure.

Physical Chemistry for first year pharmacy students

Studying some inhibitors (herbicides) for a plant enzyme. Looking at the structures of the inhibitors and how they interact with the enzyme. To design better inhibitors by understanding the interactions at the site of inhibition.

We need the software package for demonstration to our postgraduate students in medicinal chemistry. Specifically, the software is needed for drug design and discovery projects and courses.

This is a molecular biology research lab at UC Berkeley. We are interested in using your software to augment our molecular visualization abilities. We are happy to cite you in all publications where your software is used. This is our first application for a license.

Wish to use the calculation packages.

Teaching Organic Chemistry, Stereochemistry, Advanced Organic Chemistry, Bioorganic Chemistry.

solubility and dissociation calculations

My PhD thesis revolves around a novel small molecule inhibitor and it\’s interaction with a protein. I will use the software to provide me with as much chemical information as possible about this small molecule.

student

Teaching regarding DRUG DESIGN AND DRUG INTERACTION

CERMN (Normandy Center for Research and Studies of Drugs) is specialized in the design, synthesis and development of new potential drugs. A new interface for managing our in-house chemodatabase and calculating molecular descriptors, fingerprints, protonation states… is in progress. We are also part of the National Chemolibrary (http://chimiotheque-nationale.enscm.fr).

To write lab reports.

The software will be usefull for measuring and drawing several different organic molecules. It will help to schedule models of molecular layers and by doing so, help to understand AFM images better.

Study ligand-protein interactions.

I teach basics of quantum chemistry and fundamentals of molecular spectroscopies and advanced courses in vibrational spectroscopies and their application. I would like to use your software in my teaching practice either to improve my lecture notes or to give a possibility to my student to use the in their projects. My main interest in research covers nearly all areas of vibrational spectroscopy, but the main one is the structure of metal carboxylates, which led to me to the metal organic frameworks.

Chemoinformatics/Bioinformatics

The avian influenza virus (subtype H5N1) is currently becoming the world\’s largest pandemic threat due to the high lethality, in birds and increasingly humans, and virulence of its endemic presence, its increasingly large host reservoir, and its significant ongoing mutations. The two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA) of influenza A virus, play an important role in the interactions with cellular receptors containing terminal N-acetylneuraminic acid (Neu5Ac, or NANA) moieties, aka, sialic acids. The approved anti-influenza drugs, oseltamivir and zanamivir, inhibit H5N1 activity by targeting the NA active site. However, research has shown that antigenic drift may result in viral resistance to the abundant presence of existing NA inhibitors through the retention of Neu5Ac moieties by complex glycan near HA receptor binding site; and antigenic shift could give rise to new virulent subtypes of the flu virus. Thus, it is crucial to design novel HA- and NA-targeted inhibitors, which can be used in combination for optimal prophylaxis and treatment. The Relaxed Complex (RC) scheme and Molecular Dynamics (MD) simulations have been carried out on the two target proteins in the hope of capturing key protein dynamics information and accounting for receptor flexibility. Research is under way to take advantage of novel loop flexibilities and changing cavity shapes adjacent to NA active site to discover novel NA inhibitors that may work in a way similar to the HIV integrase inhibitor, raltegravir, inspired by the RC/MD simulation procedures. Further investigations involve HTS virtual screening (VS) and hit optimization of the VS results through QSAR type statistical analysis in conjunction with ChemAxon suite and diverse ligand libraries.

Investigate the P-N Bonding Model in Metal Complexes My project is to understand the P-N bonding structure with the following structure;Any metal complexes with a PN ligand on it; the PN ligand must have 2 identical substituents on phosphorous and 1 substituent on nitrogen. In the early paper, they suggested that the bonding between P and N involved using the d-orbital.1 However, it had been rejected recently. They suggested that there are negative hyperconjucation between the lone pair electrons on the nitrogen and the P-X anti-bonding orbital.2 My project involved retrieving X-ray crystallography data from Cambridge Crystallographic Database (CCDC). The P-N bond lengths are compared with P-X bond length, N-X bond length and other factor. In order to rationalize the bonding property of the ligand, different substituents on P and N will also be looked at. References: 1. H. R. Allcock, Chem. Rev., 1972, 72, 315 2. A. B. Chaplin, J. A. Harrison, P. J. Dyson, Inorg. Chem., 2005, 44, 8407; H. Sun, J. Am. Chem. oc., 1997, 119, 3611

Assistance in developing analytical methods for residues of veterinarian drugs

1. to cluster library of compounds used in drug screening project 2. to cluster building blocks used in comb lib

Research into modelling blood brain permeability of drugs

I\’m a student much interest in programs of chemistry, because they are very useful in my graduation (pharmacy and biochemistry).

I was teaching bioinformatics.

We are using the ACE Organic software in undergraduate organic chemistry courses. I would like to students to be able to do conformational analysis on simple systems.

I joined the Chemistry and Biochemistry department at San Francisco State University this fall and am teaching all the General Chemistry lectures in addition to a lab course. Next semester my teaching duties will be expanded and will include course resource development for the department. I am looking for an easy to use mac-based program for drawing structures and showing them in various configurations (ball and stick, wire and 3D for example). I plan to use this for the following applications (1) structure drawing to add to my powerpoint lectures (2) structure drawing to add to my course website more importantly (3) use this as a tool in class to help students visualize molecules in 3D and understand how basic principles (such as VSEPR and hybridization) can be used to predict basic shapes. In my current courses, which comprise about 300 students total, the students invariably get stumped when they have to begin thinking about 3D structures. I would like to have some tools to use to help them with what has traditionally been a big stumbling block for them. We have some new equipment at SFSU to create 3D movies as a visualization tool. I\’m not certain if any of the ChemAxon products are able to be tweaked in order to produce the input I\’d need for programs such as GeoWall, but this is another thing I\’d use it for if it does have that capability.

I am an academic staff, teaching medicinal chemistry and organic chemistry. I\’m using Linux for my studies and I would like to try JChem how it works!

Marvin Sketch is used as an input sketch tool for the ligand depot research tool for searching the small molecules in the Protein Data Bank.

I intend to use the tool to assist me in development of pharmacotherapeutic aspects of our research pertaining to prodromal markers for neurological and psychiatric disorders.

The aim of my teaching is to better teach students Organic Chemistry On-Line.

I\’m currently designing a course (Technology in Science Education) in the School of Education, and am evaluating various software packages to see if they would be useful either: to high school teachers of physical science; for designing pre-made materials the same set of teachers may use.

I teach a Master Degree level course on drug discovery, focusing on the use of informatics tools. I want to use Marvin in this class to illustrate principles of chemistry and cheminformatics, and am interested to also encourage students to explore Marvin. I will only be using the software on a MacBook computer for teaching purposes. I do not plan to make any website implementations of the software.

For new products, we determinate experimentally, by capillary electrophoresis, their pKa. We like to compare with theorical data the experimental values.

Intended for use in development of QSAR descriptors for ligand-based drug design research project. Particular interest in logD calculation tool.

Current research is focussed on mechanistic organic photochemistry, including photoinduced electron transfer processes and the self-assembly of natural pigments.

we are going to teach graduate students the application of computation chemistry in functional food area. Meanwhile, we have two projects on disclosing the mechanism of phytoestrogens\’ binding to human estrogen receptors. We need use softwaresprovided by Chemaxon.

1. Chemical databases: (i) similarity and (ii) substructure searching, (iii) clustering, (iv) filtering 2. Ligand-Based and Structure-Based Virtual Screening 3. Post-HTS analysis 4. Molecular Modeling 5. Molecular Descriptors implementation: (i) 2D, in particular fingerprints, and (ii) 3D 6. (Quantitative) Structure-Activity Relationships

Molecular modelling, self-assembly

Studient

I am a student of Yizeng Liang. Alex Allardyce will give a cheminformatics seminar series to be held at our university locations next year,so I need a licence

I actually am a student at St. John\’s university and i need the program for my organic chem class. we have mandatory quizzes on the ACE organic website. I need the program to display all the isomer conformations for certain questions.

The tools will be used to build QSAR models based on high throughput screening against yeast strains. These models will be used to identify other molecules to be screened, and to try and explain the mode of action of the compounds.

We would like to use the react/synthesize tools and associated reactivity/selectivity plugins to create a freely downloadable reaction database. The reaction database will only include reactions between molecules in publicly available compounds that also produce publicly available compounds.

I am research assistant and studying computational chemistry so ı want to use your program

Since we are working on structural biology. In a first site the software attracts us to explore. We want to use the software for modeling small molecules and calculations for understanding their properties.

to draw structures for reports

Polymer nanocomposites refer to a broad range of composite materials. Due to unprecedented improvement observed in properties of nanocomposites, research interest in this area is growing exponentially. In designing better nano-composites with tailored properties some of the major challenges include understanding the structure-property relationships, interaction and integrity of the two components at the interface and the role of nanofillers in enhancing the properties of the composite. In our work, we utilize atomistic simulations to address these issues and develop structure-property relationships for an amorphous aromatic piezoelectric polyimide substituted with nitrile dipole and its carbon nanotube based nanocomposites. We aim at developing a better understanding of the physics of polyimide-nanotube interfacial interactions and use it for designing nanocomposites for advanced applications, through ab-initio quantum chemistry, molecular mechanics and molecular dynamics calculation. All the MD level of work is primarily done through LAMMPS. However for presentation purposes, a visualization tool is required for molecules, the structure evolution. Also it is nice to have a software with visulazation capabilities to run charge calculations, Molecular dynamics, polarizibility calculation on small scale in personal computer to assess different parameters to be used in large scale simulation in LAMMPS. (http://lammps.sandia.gov/)

I would like to construct a website for high school children, to explore some structures to aid them with their study. My father is a high-school teacher in the UK and it would be in-conjunction with him and not affiliated to UPenn. I am not sure if this is the correct license application for this purpose. Many thanks

I am a student use ace organic for homework and wanted to use some of the features for in class assignments

Construction of linkers between nucleotide and amino acids

For use exlusively by UK academics for their research. Access will be free at point of access and user will require an individual ID and password. Database will consist of chemical supplier catalogue data. I have spoken to Alex Allardyce about my status as an academic and the software will only be used for academic purposes. There will be no commercail access allowed.

I am student

I plan to use Marvin for pKa calculations and structural modeling as part of our anti-parasitic drug development research program.

Chemical molecule building and visualization, molecular geometries and hybridization visualizations, polarity, etc. Intended for student use and graphical manipulation of molecules.

Biochemical research on poly(ADP-ribosyl)ation is performed during a 3-year PhD project. The software will be used to draw sketches for personal clarification mainly. So far, no publications are planned using the software.

I plan to use this program in the general chemistry course when looking at geometry of molecules and in physical chemistry to compare physical measurements with calculated ones (like log P).

Molecular database mining of (GPCR) ligand databases.

I\’ll use the software to built a datatbase of our extracted naturals products from cold water

Use for A2 Chemistry

Calculating physico-chemical properties of organic molecules

I will use this tool to do a case study on drug design and discovery class. I am going to design a small molecule inhibitor binding to the receptor tyrosine kinase c-Met. So I\’ll use this tool to display the 3D structure of my inhibitor and show its chemical characteristics.

A\’Level Chemistry teaching and BTEC Diploma Chemistry teaching.

1) Teaching medicinal chemistry an introductory course. 2) Medicinal chemistry research: The design of novel bioactive compounds. Apart from the development of synthetic routes to the desired compounds, we also incoporate physico-chemical properties to aid optimising the compounds as well as in explaining QSAR studies

The research mainly involves generation of viritual chemical database and library analyses, using molconvert and cxcalc. For the teaching, mview and related plugins will be mainly used for demonstrations in the class room.

I would like to evaluate these products. I will describe any uses after a full evaluation. Thanks!

Our group is an interdisciplinary unit which invents, synthesizes, characterizes, formulates and tries to promote therapeutic systems based on synthetic polymers which are biofunctional, biocompatible, degradable, and sometimes bioassimilable. We would like to have more physico chemical informations about the chemical products we have working with.

optimisation of small haloacids

research on drug molecular properties and extrapolation of physiochemical properties of different molecular configuration

Cheminformatics

i am studying chemistry, i need this powerful software to help my study. please give my liscence.

Attempting to install the ChemicalInventory package from SourceForge. My group needs inventory software with structural search features.

I need a package for drawing molecules, including organic molecules, to be used with Chemistry exams.

I am a student and i am trying to learn Marvinsketch after which i could also explain it to my classmates.

I would like to possibly have the full use of this software to aid in developing more of a visual presentation to my class which is currently lacking. Hopefully by introducing software such as this, I can stimulate interest into chemistry and the implementation of computers to aid in molecular modeling and calculations.

I am trying to bring a different light on chemistry to my students. It is often hard to imagine and to understand stereoisomery and molecule structures, so I think that Marvin is the best program to make them like chemistry even more.

To look at 3 dimensional structures of water-soluble monomers and to anticipate if water molecules can fit into molecular cavities

Use JChem to aid understanding primarily in organic chemistry and conduct research in Spring 2008.

Virtual screening of potential ligands of HSP90 and CA proteins.

I will use the software for chemical informatics based research, the main focus of my PhD. I am interested in data processing, descriptor calculation and machine learning based classification.

Use of MarvinSketch in teaching as tool to draw 2D structures and calculate chemical properties and IUPAC names of molecules; use of the pKa Plugin to predict acidity of organic acids in my researches

Coordination chemistry : study of complexes formed by tetraazamacrocycles with lanthanides ions (luminescence, potentiometry, EXAFS…)

My reacherch interst is understanding a selective toxicity of neurotoxic compounds on invertebrates over vertebrates.

will be used to help with my degree course

We currently have ChemAxon Marvin tools on our Macintosh computers in the computer lab at the Thomas Cooper Library at the University of South CArolina for use by students, and would like to offer the calculation tools as they have been requested several times.

Senior and IB Chemistry programs

I\’m calculating molecular structures and properties by using QM method. And I want to find the global mimimum by using conformations plugin.

We are currently focused in two principal areas: Matrix metalloproteinase inhibitors and selective strogen modulators. We would like to store the compounds we have and also the compounds we are getting from synthetic processes.

I teach a biomaterials course in the Faculty of Dentistry and I frequently present and discuss structure-property relationships. Access to the software is quite useful in my research.

Sketching, drawing and viewing structures and evaluating their properties, etc. using calculator plugins. The aim is to get a preliminary evaluation of the molecules under study for our biosensing work.

Biochemistry molecule structure and synthesis

to draw scheme for the newly synthesized compounds

Teaching in Nutrition Science and Pharmacology Research on the effects of bio-active lipids on metabolic syndrome

Calculation of logP, logD and pKa values. Structure activity relationship studies. Classes with students aiming Physicochemical Analysis in Drug Design for 3 year Pharmacy Students

Optical resolution by photochromic adsorbents. Stereochemistry of carbon compounds may have some influence on the pharmacological activity within a living organism. Optical resolution and analysis of chiral drugs have been critically important, since one of the two enantiomers may cause serious side-effects. Liquid chromatography is one of the most useful methods in optical resolution and analysis, which depends on the interaction between the chiral medicine and packing adsorbent. Photochemical control of adsorption ability in a reversible manner is now under way.

Pharmacophore descriptors (sorry guys, I\’m iin a hurry today, can\’t fill it out properly!)

usage for all aspects of studium of general, inorganic and physical chemistry

The program will be used for predicting physico chemical properties of compounds that will be screened against various targets.

We have developed a database for chiral chromatography (using ISIS/Host software).We used ChemAxon tools to evaluate the molecular diversity of the database (see reference below). We are now evaluating the similarity search using ChemAxon fingerprint tools (this works fine and may allow us to write soon a paper). We also built a small Jchem public database containing chiral drugs and freely accessible on the web. We would like to obtain a license which would allow more than one search/minute (only for this database; we do not need any structure search for our non public databases as we just use Isis/base and ISIS/host) I may also suggest our University to give courses on ChemAxon application.

Area of metabolomics in order mainly to mine out and clean molecular pathways

we try to create a new compounds have good beta blocking activity especially after the separation of beta2 receptor 3D structure

Will evaluate for use with chemistry course that taught- hope to use with smartboard expansion to further develop

HTS for compounds active against Plasmodium falciparum malaria.

Drug discovery (virtual screening, lead structure optimization). Biocatalysis (enzyme specificity).

Reseach: polymer synthesis

My research projects involve: exploring chemical space and prediciting physiochemical properties of small molecules. I expect to use this software for physiochemical predictions such as logP and pKa and application in a 1cellPK model.

we are trying to exaine the relationship between molecular structures and drug toxicity.

Use of software in AP Chemistry class when students are studying various topics, specifically organic chemistry.

My main fields of research are computer-aided drug design and computational chemistry, including docking, screeneing and molecular dynamics simulations. Teaching subjects are related to these themes as well as protein structure and energetics.

The research aim is to better understand why some molecules bind to the active-site of penicillin binding proteins (penicilins, cephalosporins), and why some molecules are not able to bind, in order to propose ligands for resistant-strains penicillin binding proteins. We need standardizer and some tools from chemaxon to clean virtual databases so that we can work on molecules ready to react with an active-site. We envisage to use some tools implemented in chemaxon by Sylvaine Roy and Samia Aci that work nearby (CEA Grenoble).

I want to simulate the suface of some semeconductor. The simulated resulats will be input file into DFT simulation.

AD and estrogen

I am developing methodologies for catalytic, enantioselective diels-alder type reactions and need an adequate modeling program

I\’m currently involved in molecular modeling, QSAR and drug design using molecular mechanical (MM2 software) and quantum mechanical methods (MOPAC, CS Gaussian Client software).

The software will be used to analyse the structure of certain organic compunds like phenylethylamine, benzene to find their molecular size and stereoisomer structures. All this data is required for a courswork report for the subject. This research is totally academic and will not invole any sort of commercial use whatsoever.

I am a physical organic chemist, interested in studying the mechanism of phosphate ester hydrolysis. Your pKa calculation tool is so useful. Also, I have started using MarvinSketch in order to generate pictures for publication and will be citing this fact.

Our main research focus is in the area of antimicrobial drug discovery. It involves screening of large small molecule libraries in the search for novel antimicrobial compounds and then we further characterize their targets and mechanism of action. This is the first time we\’ll be using this package but we beleive (based on the tools description) that this software package would provide various tools that would help us in our studies. To name a few, this includes structure editing and viewing, pharmacophore perception and virtual screening, clustering and diversity calculation and many structure-based applications.

Used to show structures within a classroom

Teaching Computer Chemistry. Using the Marvin software because it is compatible with various platforms (Windows, Mac, Linux etc.). Using it in our computer pools and for the students at home and on their notebooks.

I teach AP chemistry and Honors chemistry courses and this software will be used as instructional aid.

I wish to use the software to teach aspects of chemical bonding, structures and nomenclature

The Education Group at the Chemical Heritage Foundation develops web-based materials for use in science classrooms K-16, especially grades 6-12. The educatonal materials are offered free of charge to all users of our web site. We also present workshops at various science teacher conferences across the country to expose teachers to our materials, and to train teachers in their use. The Chemical Heritage Foundation is a non-profit organization.

My research is involved with chemical structures of various compounds. Therefore I need a program to draw the structures

We have a number of students working on ionic liquids. They have expressed an interest in the calculation of log P, log D, pKa, etc. Lafayette College is an undergraduate specific institution and so all our activities (classroom or laboratory) are teaching centric.

Design animations to use within school to accompany our GCSE science syllabus. Having just retired, and then been asked to go back part time I \”should\” have more time available to develop simple ict programs that will help in the understanding of science, especially chemistry.

I am teaching AP Chemistry, Honors and Regular Chemistry and I find this a very valuable tool for teaching Organic and biochemistry, particularly the structures of the different molecules.

The software is to be used in one year one subject on biophysics and biochemistry. Students are expected to learn how to build molecules on computer and output structure for QM/MD calculation. Also, one year three subjecct will also utilize the software for advanced topics and molecules.

I am currently researching pKa prediction methods and would like to utilise this implementation in your software.

I will be working on protein-ligand docking for my dissertation and will require tools to create/visualise the ligands. If possible, I will also need to perform energy minimization or any other manipulations on the ligand such as to achieve a more optimal docking.

Powe point presentation s about Organic Chemistry undergraduate courses for Biotechnology and Pharmacy

Modelling porphyrin structures.

I am currently using Marvin as part of the ACE and I want to utilize it for most of my drawing needs plus other capablities like conformation and isomers search. I am also a computational chemist and I want to evalaute these plugins to see how they can help in a conformational analysis.

I would like to use this program for supplemental instruction for myself and classmates.

Organic chemistry courses I teach and bioorganic chemistry research with undergraduate students. Research focuses on polymer-supported thiol reagents involved in protein folding.

Departement Chimie

The software would be used to compare diversity between two datasets.

to find better visualization and calculate the property of my proposed molecules.

Create a medicinal chemistry text incorporation organic chemistry / reaction mechanisms, incorporate appropriate biochemistry (ion channels, transport mechanisms, etc) and apply biotech processes or molecules to description of molecular moieties used as drugs in humans and/or domestic animals.

Instruction of undergraduate and graduate students in organic and biochemistry

We plan to evaluate ChemAxon\’s software in the context of ligand preparation for docking calculations. If it proves useful, we may incorporate instructions on how to use it into free tutorials we disseminate through our web site (http://autodock.scripps.edu) and occasionally give from time to time.

My name is Sandra Kreitner and i am a Ph. D. student at the university of Regensburg. I want to create a database for a virtual screening with the Instant JChem 2.1 program.

Knowledge of pka of widespread functional groups of drugs is important for a molecular understanding of bioavailability (solvation absorption etc) so that students are able to derive these important features by a given hit or lead drug structure.

My lab develops small molecules targeted to cancer cells for early diagnosis and staging of human cancer. We are creating an integrated set of 6 robots to automate the synthesis and screening of combinatorial libraries. JChem will be used to enumerate combinatorial libraries that we design, to store chemical structures, and to eventually, if we ever get any hits, to help decide on the next best libraries to synthesize.

Synthesis and antibacterial, antifungal , antiviral activity of Thiozolidin-4-ones derivates

presentations and visualizations for classrooms

I will use this applications to create ligands for a receptor protein involved in a viral disease. I\’ like to use those ligands in docking experiments and possibly MD simulations

Molecular topology descriptors, QSAR/QSPR, drug design, molecular similarity, data mining

Synthsis of functionlized poylmers characterization of polymers

I am working under Dr. K. Uma Maheswari (Asst. Prof.). I am trying to find potential anti-HIV lead elements. I am focusing on Reverse transcriptor Inhibitors, Entry Inhibitors, and Fusion Inhibitors. I want to screen the pharmacophore model for similar lead molecules.

Learn about these tools, to develoope research and teaching opportunities, relative to sensor based applications.

The aims of the research is purely scientific, with no commercial interest.

I plan to use Marvin Sketch software and licensing in aid of designing HIV-1 integrase inhibitors. Specifically I plan to use this software to easily transfer molecular structures from databases, then visualize and help determine binding mechansitics at specific integrase residues.

Drug analysis.

Mainly to optimize sample prepartion of pharmacueitcla compunds

I am a first graduate student. My project is screen chemical.

Interested in finding novel mechanisms of HIV protease inhibition by virtual screening libraries of small compounds. This will aid understanding of the sequence variability and biological function of HIV protease.

We do research in Inorganic/organometallic chemistry

Drug designing Studies

Sorption of organic compounds of various molecular structures.

I currently teach Biochemistry to first year medical students and your company\’s applets would serve as a power tool to demonstrate various chemical structures, especially for the enzyme inhibitor lectures.

Our aim is to bridge the gap between quantitative protein chemistry and cell biology: * focus on protein folding and quality control in the cell and to apply techniques ranging from spectroscopy to microscopy * maintain a tight link between cell biology and the hard-core biochemistry in approaching these problems We are in particular interested in thiol biochemsitry and are developing new reagents for our work.

I am teaching university students the plant molecular physiology in the biochemistry department. For preparing a printed material or a visual presentation, I often need to draw chemical structures. I have been long searching a good chemical drawing program on MacOSX. I would like to utilize your software for my teaching purpose.

We\’re interested in developping LC/MS-MS method for determination of drugs monitoring (especially in tyrosine-kinase inhibitors)

molecular modelling of polymerization reactions

For use in teaching structural chemistry to high school students.

Principally for exploration & an easier alternative to more complex alternatives.

I want to see and learn this interesting.

I am working with Dr. Doemling to develop a database of multicomponent reactions in IJC.

I intend to use your software to assist me in the completion of my Ph.D. research program in Chemistry. Specifically, I would like to use your Marvin drawing software for writing my dissertation and for 2-4 scientific publications.

Working with large combinatorial library synthesis using peptoids on DNA.

This is a course on Molecular Modeling, and wish to show to my students the current status of modern software, integrating distinct modules with powerful capabilities, web-aware. Your product is ideal.

As student using the program for calculation of miscellaneous substances used in exam-projects.

We are developing fragment based drug discovery methods in academic setting. We will use ChemAxon software to analyse and characterise our compounds and to convert between various formats.

Chemaxon software will be used to calculate physicochemical properties of compounds for computer simulations of pharmacokinetics.

materials science

I research in QSAR, with Topological Descriptor

I am doing academic research of enzymes mechanisms and the development of the methodology of drug design. I have one doctoral and one master student, so to teach them the profession I would like they will be familiar with the ChemAxon\’s Academic Package.

I am a student studyin chemical engineering and i find the software you provide very useful to get more insight in certain fields of my study

We have started a new Computational Chemistry Research Group, and we would like to use this in our Lab

Molecular Dynamics simulations of hydrogen transfer processes in enzymes

I teach web-supported face-to-face and online biochemistry, molecular biology, and non-majors science classes for biology majors and general education students. Many of my students become science teachers. I am full-time faculty in the College of Arts and Sciences. We are not a research university in my discipline. I plan to offer my implementation first in Blackboard CE6. I could also make implementations available on my faculty web space.

Course on Drug Design

The software will be used to enable students to describe compounds and their physical chemical properties and where relevant relate it to their environmental impacts.

We are currently working on the design and synthesis of chemical vectors for DNA and/or drug administration. These products are amphiphile and charged compounds, calculations offered by your tools will be very useful for our design and predictions of new compounds

general chemoinformatics – drawing structures, converting structures for similarity searching and QSAR

To be honest, we don\’t have an implementation plan yet. We\’ve just started using OWL (UMass Amherst) for our intro Organic course. We are impressed with how Marvin Sketch in implemented, and we thought it would be interesting to see how we could incorporate web-based learning modules for laboratory preparation and for more advanced courses (including some computational interfacing). I don\’t know what this will look like; I\’m just exploring right now.

i am student of material science and need a good program to draw chemical reactions for my protocols. i found marvin sketch and would be very glad to get a license.

Research in Cancer Disease Field

I am trying to use it to teach high schol chemistry and to allow students to see the 3-D aspects of organic chemistry. Also hoping to find a moodle plug in so that students can draw diagrams during a test.

Comparison of various ionic channels modulators.

I would like to present the logP, logK prediction in the education with your software under the practice lessons.

block polymer composites

The software will be used for teaching chemistry and biochemistry in School of Medecine and Medical Technology School in UEH, particularly the Course of biochemistry offered online (Moodle platform).

Chemaxon tools are used in a system of automatical determination of the 3D structure of biological molecules.

Chemical structures, reaction mechanisms

Polymer and Fiber Chemistry

Organization and categorization of a small molecule collection for HTS.

Analysis of novel enzyme cofactors.

I will be teaching science education, and for my own learning and subsequent teaching I believe this would be very useful.

I am teach chemistry, I want use it to draw structure of molecule.

just checking it out

I am a organic chemistry student at Virginia Commonweath University. The instructor is using ACE Organic 1.5. I need the license keys for the \”Tools\” in Marvinview particularly the Isomers.

I am a teacher for biology an chemestry at Augsburg near Munich.

QSAR teaching

I want to use Marvin to get the molecular surface area of differente ligands to compute the energy contribution of some functional groups.

We are installing an intern database of our chemical stocks using chemicalinventory.org software and it requiere chemaxon.

It\’s going to be used during my laboration course in advanced organic chemistry.

Pharmacogenomic screens in yeast.

Chemo and BioInformatics research at the UNC – Chapel Hill (Supervisor: Pr. Alex Tropsha), in continuation with my previous works at the laboratory of Chemoinformatics of Strasbourg (Supervisor: Pr. Alexander Varnek).

In our laboratory we work with drug design. The marvin program is used for drawing structures and analysis of protonation and conformation state.

Used in the UMBBD website, http://umbbd.msi.umn.edu

My research is about Quantitative Properties (Glass Temperature) and Structure for polymer.I need your tools to calculate geometry analysis for some polymer,and it will be used as descriptors.

Stimuli-responsive polymer conjugates for biological applications.

Using primarily to draw chemical structures.

online courses on organic chemistry and on classroom evaluation of tools

Class Research

management of monomers for the synthesis of a large (10^15) member chemical library.

Drug analysis baseed on the clustering

As an organic chemist, the first thing that interests me is the pKa calculations through marvinsketch. This seems to be a convienient and accurate tool for pKa determination. I will also be interested in tautomer/resonance structure generation, partial charge determinations, conformer generation, 3D structure generation, file interconversion, minimisation and dynamics in one easy to use package. If this packages abilities prove satisfactory i will definatley be citing in publications/presentations wherever possible and promoting the package to collegues. I hope also to give feedback for the development of this project.

General Organic chemistry

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education

education

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Education

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Education

Require to calculate logP and pKa of novel prostanoid ligands. Also wish to view Marvin models.

I would use the Marvin software to draw structures of the chemical reactions I will be performing in my research, for use in presentations and possibly publications.

all type of catalysis

Création d\’un cours sur powerpoint pour les étudiants

Used to show protonation sites and species distribution

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Use this kind of software for reasearch in areas such as Organic Chemistry , Physic-Chemistry and Biochemistry

Educational Presentation

test converting moleculars to diverse formats.

For a number of subjects, including biotech and medicinal chemistry some of your tools are simply invaluable for looking up the pKa etc. Your tools will be used for course assignments.

Conducting research into drug metabolism and bioanalysis and looking to use the software to predict pKa values of analytes.

Research on the prediction of Log P.

Our research and teaching areas are chemical crystalography and biochemistry. We are currently working on the structure, biological function and activity of protein isolated from mexican plants. We also carry out drug design studies of some important natural products involved in the treatment of diabetes and rheumatoide artritis.

teaching Advanced Analytical chemistry and physical and chemical separation courses for grduate student. research: 1- determination of protonation constant of organic acid and drugs. 2-Studyof liquid membrane transport and mechanism of transport. 3- Application of ab intio method for predicting physico-chemical properties and QSAR/QSPR

bioinorganic materials, study of biomineralisation processes, modelling

Electrochemistry

generation of rough geometries of molecules for ab initio calculations

• Evaluate Chemaxon more fully. • Make the contents of our structure database more easily available to campus users. Integrate the display capabilities of Marvin with our database searching. • Build Chemaxon’s functionality into our Assay Exploration System (Assay aggregation and query system). It should be independent of any structure database but use JChem by default. • Pre-generate descriptors for searching. Create plugin wrappers for descriptors not available through Chemaxon e.g. ALogS.

I am a protein crystallographer with research interests in structure base drug discovery and structure based functional prediction. I have been impressed with Marvin for manipulating and viewing chemical databases but have not used it to search active sites and identify potential compounds of interest. I am interested in the enzymes of the shikimate pathway as potential antimicrobial targets. I am also constantly looking for appropriate software for teaching to try and educate chemistrys and medicinal chemists about 3D structures and how a solidf understanding of structure is necessary for effective synthesis of inhibitors.

organic chemistry, 1st and 2nd semesters

I am doing science in the fascinating field of virology and biochemistry. I am pursuing studies of inhibitor development of HIV proteins like the protease using the phage display technique. Our goal is it to use inhibitors to define mechanisms of virus maturation and resistance development. Therefore, the application of your software would be well suited. The presentation of chemical structures of inhibitor and small inhibitory peptides would be really helpful. Furthermore the characterization or prediction of small peptide features using your software would be a great support for our study.

The software will be used for calculating the charges of biochemical compounds for reconstruction of metabolic networks.

Calculation of dissociation constants

Construct a database of small molecule with their biological, physico-chemical, and molecular descriptor properties. For Knowledge extraction and Data minig for virtual screening

I intend to use this software to builded chemical structures and/or view the results of the ab initio calculations for the teaching purposes. I am in process of developing experiments for the physical chemistry laboratory. My research concentrates on the electronic excitation energy transfer in DNA. I would like to use this software to view structures and MOs.

Computer Aided Drug Development for antiviral drugs

It will be helpful for understanding the VSERP theory in my class. Student can actually assemble a molecule model and can confirm the structure.

I will be using ChemAxon products for optimatization of 3D structures, naming molecules, and drawing any other structure relevant to my research.

We need a chemical software for teaching students which are making their diplomas in our institute, writing parers and research reports.

Software will be used for registering new compounds into the University compound database

I am teaching physical chemistry course

Thank you

To provide further insights into biosynthesis of proteoglycans

Used in teach Pharmaceutical Engineering course (PharmSci 519) and PhD Pharmaceutical Sciences course in Fundamental Properties of Solids (PharmSci 754). Goal of teaching is to deomonstrate the utility predictive tools for pharmaceutical scientists.

Developping interactive organic chemistry learning, using free software opportunities, to introduce to organic chemistry, 2D & 3D representation of hydrocabons and principal fonctions, introduce nomenclature (for 2nd year of high school students), introduce structure and reactivity of organic compounds and reactions, introduce basics of chemistry of life (for 4th year of yigh school students). Actually using multiple limited software like Chemsketch, Viewerlite, swisspdb viewer…which are time consuming to introduce and use

Educating and Training for chemistry teachers

pKa measurements

Creating chemical formulas. Generating conformers for usage in MD calculations.

I study on computations (Gaussian) and i also want to have a general knowledge about chemaxon.

We have a group of young scientists who just started to study molecular modeling also with my supervision.We need number of available tools. Presently we have academic license for MOE and Grid. I have an interest in clustering tools implemented in JChem, JChem Base and JKlustor.

I want to use this software to sketch structures for my students and to show them 3d structures with charges.

Drawing structures for use in documents and web pages Calculating numbers for use in teaching and assessing Possibly developing interactive pages for teaching using MarvinSketch

Study of carotenoids. Draw chemical structures and log P calculation.

We hope, this academic package will be useful in teaching process and help us to explore the physical and chemical properties of biologically active substances.

I research about biomedical engineering. For example, bio sensors, cell adhesion, immobilization of biomolecules and so on.

I teach a medicinal chemistry and molecular modeling course. These courses are designed to teach the fundementals of drug design and drug discover. A range of approaches are used from Hansch/Topliss to CoMFA, docking, de novo design based on the structure of the receptor. Students will be able to state the approaches used, be familiar with a range of software packages available for drug design and molecular modeling, and design drugs either de novo or based on a lead compound.

I will be applying this software to complement the neuropharmacology laboratory practice for setting up practical software for computational neurochemistry. As for teaching, it would be also useful for characterizing 3D visualization molecular systems, and analysis of molecular structures.

My group is focussed on docking algorithms in an academic environment. We have designed the EAdock (Grosdidier, Zoete, Michielin, Proteins 67, 1010, 2007) docking software and would be very interested in using your software suite to handle our compounds. Thank you for making it available for free to academics, Best regards, Prof. Olivier Michielin

Quantum Biochemistry class

Studies on modern trace analytical methods for the identification of emerging chemicals and not yet investigated residues in the Arctic environment. An important part of the course is the evaluation of chemical structures with regard to their ecotoxicological and environmentally adverse effect potential

None at this time.

Computational chemistry projects

I study organometallic catalysis including there development and synthesis. Molecular calculations are also used to get information of the catalysts.

molecular modeling and visualization

molecular orbital theory

I\’m teaching Analitical chemistry 2 with laboratory where some concepts regards acid-base equilibria and solubility are present in my program. Moreover I would evaluate this software for chemical properties calculation in complex environmental compounds (ex coprophorphyrin)

My independent study students will use this package to minimize the energy of three-dimensional structures that they construct.

med chem research

I\’m taking a organic chemistry class right now and this software would really, really help me in understanding some of the things we\’re going over in class.

I am doing research about pKa analysis using electronic surface descriptors. The software is needed to make my new approaches sounder and compare them to well established approaches.

Evaluating for teaching chemistry

Using marvin to prepare small molecules for docking studies.

Our aims is calculating chemical properties of small molecules for docking simulations.

Plane is to set up a molecular graphics teaching lab for undergraduate pharmacy students. Introducing students to various aspects of molecular drug design. First step is to gain the ability to design, contruct and manipulate molecules on screen.

Now I am doing some research about interactions between ligands and proteins. In order to obtain the better results, I need to know the protonation of the ligands. Therefore, I wanna use your program to calculate the pKa values of the ligands. The major goal is to publish our result in an international journal.

drug development (adenosine receptor antagonists)

I will install the softwares on my iMac and my Macbook and use them for writing handouts for my classes as well as for demonstrations in the classroom. The material crated with the softwares will only be used by my own students at school.

Development of teaching materials that help pharmacy students to understand structures and effects of drugs.

I am evaluating MarvinSketch for use in teaching chemistry. I teach freshman and biochem, but I may suggest to my organic colleague that he look over the package as well. Implementations: 1) use in developing notes for students 2) develop web-based delivery of chemistry notes for freshman chem (I\’ll have to learn how to make animations and better understand the capabilities of the software) 3) if license allows, I would like to develop a lab for freshman where they learn to use a chemical drawing package and investigate the physical properties of a few molecules. The students are usually surprised that chemical drawing packages even exist. Implementation 3 would require that the software be installed in the computer lab on ~14 machines. If successful, this would make a nice research project suitable for publication in JChemEd.

I work with, and develop, quantum chemistry computation methods and software. The Chemaxon programs will be used as handy tools for visualization of structures taken from the web, modifying them if needed, converting various structure formats etc., for molecules I am studying in my research or just use as application examples for testing my programs and methods. I do not presently intend to implement your software on our site, or to develop any applications that use your software.

research covers six Membered And Seven Membered Coumarins, Benzopyrans, Flavones, Chromans, 4-Thiazolidinones, Pyrazolines, Pyrimidines, Dihydropyridines, Isoxazoles, 1,3,5 Oxadiazoles, Thiadiazepine, Triazoles, Sym. Triazenes, 1,3,5 Thiadiazoles, Cynopyridines, Quinazolones, Quinnzolines, Quinidines, Isocoumarines, Pthalazinones etc. Calcium channel blocking, Potassium channel opener Anti-cancer, Anti-viral Reverse transcriptase inhibitors Anti-integrase, Anti-coagulants, Antithrombic

organic chemistry

Drug Design course teaching. Drug design for HCV genotype 4 management

Our group focuses on organic bio-electronics. The field relies heavily on the interactions between charged molecules and polymer hosts (which often have variable or unknown pH). For this reason, we are interested in the pKa analysis package of Marvin for investigation of ion and host interaction. Of course, we are also interested in its various other capabilities.

Calculation of the pKa, Charges, logP, Surface area, H Bond Donor/acceptor, etc.

chemical discovery

Inorganic Biochemistry and molecular structure

computing pharmacokinetic properties for drugs discovery, preparing database for virtual screening

I would just like to see the electrostatic potential map

Molecular modeling. Protein-ligand docking.

My research group has identified the first modulatory ligands for a novel protein structure in the brain, and we are now interested in expanding on those hits in part with a virtual screening effort. To do so, we are constructing a fairly substantial virtual library and are interested in using the Marvin / JChemBase family of products support our efforts.

Synthetic organic chemistry including high-throughput methods, parallel synthesis, etc. Construction of databases of the synthesized products.

Professor or Organic Chemistry and spectroscopy. Research in Marine Natural Products. Teaching molecular modeling and 3D structures for NOESY assignment.

I teaching Biochemistry and currently use Jmol for web visualization of amino acids, nucleic acids and proteins. I would like to try the JChem suite.

pharmacophores models and virtual screening; library enumeration and similarity search; managing and searching structures in databases

Protein protein interaction studies in MMP-TIMP complexes

Structure-Drawing for lectures

Teaching courses in Toxicology and Pharmacology to students in a professional Pharmacy program. Will use software to draw structures and reactions involving drugs, biochemical processes, etc.

Registering chemical analogs to a database

Student for Organic Chemistry

Molecular Dynamics simulations of local anesthetics

Chemical Ecology

steroid chemistry and antibiotics

Prediction of possible extraction of valuable natural products.

I am interested to use Reactor and Combinatorial chemistry tools for looking at SARstudies for new anti cancer drugs. With Reactor, Combinatorial tools, they will facilitate me to look for possible promising targets. I plan to use ChemAxon on my personal PC.

quantitative structure activity relationships

It will be used as part of a chemical inventory system developed by the former Pharmaceutical University of Denmark, now the Pharmaceutical Factulty, University of Copenhagen

For self studying

To calculate pKa

The purpose is show charge distribution over chemical structures

Study of ligand-gated ATII-Rec

Teaching involves CHEM 4150 Introduction to Medicinal Chemistry, and CHEG 5350 Computational Chemistry. Research involves the design and synthesis of molecules to treat diseases of man.

I have been dong some research on anticancer drugs. Now I have designed several new moleculars which may have bioactivites, and I want to evalue their pka and logP for references.

calculate discriptors, pKa

I am looking to use the software to determine the pKa of different molecules.

Managment of chemistry and laboratory in group involved in metalorganic synthesis.

Presentation of structures and typical reactions of organic natural products

PHD student, use this software for the new chemical products investigations.

I am doing my final year project.Some part of it requires the basic descriptor calculation ,so i need the various plug in for this purpose.

We are developing some applications focused on enzyme-catalyzed reactions that we hope to make broadly available in the future, much as the Univ. of Minnesota (http://www.chemaxon.com/forum/ftopic253.html) has done. You may review my broad research interests at http://web.mit.edu/prathergroup. I am happy to provide additional information as needed.

postgraduate students in pharmacology wish to develop an understanding of structure-activity-relationships with respect to drug partitioning across skin

Calculating pkas of compounds to better predict best pH of mobile phases for HPLC method development and drawing chemical structures.

sir i need the software to calculate varios parameters like pKa value hydration charge etc. MY project is based on SQAR

Various keywords of about my research topic are as follows: QSAR analysis, SAR analysis, Conformational analysis, calculation of various descriptor,tautomers,

A central goal of chemical biology is to harness the power of synthetic chemistry to discover and elucidate molecular pathways fundamental to cell and disease biology. We particularly like to evaluate the chemaxon software for rendering structures and potentially inputting chemical structures.

examine small molecule structures and predict pka of functional groups

well i am just a student now so the primary use will be molucule analasis, though i plan on doign some reserch with a professor here concerning organomatalic compounds and there reactants.

I am teaching in chemometrics and QSAR I am intersted in Log P calculation for QSAR prediction Thank you for your free academic licence

I am in my second year PhD (in synthetic chemistry and cell and molecular biology) and need a chemistry drawing programme to use in everyday tasks including writing reports and papers. Will be used only by myself.

calculation of log p and log d of new molecules

The software should be available for students in the workgroup to use it in laboratory practice as well as writing their reports about the practical courses.

Organic Synthetic Chemistry…for both structure drawing and analysis.

The ChemAxon products will be used to aid our research on non-catalytic oxidation (combustion) chemistry of cyclic compounds, including cycloalkanes and aromatics.

calculation of the pKa value of the charged amino acids in a group of oligopeptides need to be done

This software is very powerful in predictiing the physical and chemical properties of different drugs. In my research, I focused on the mechanism how drugs are absorbed through the biomembrane, the Chemaxon sofeware can give me very strong help.

Molecular modeling researches

Chemical drawing.

1. Teaching – training for students from Jagiellonian University, Faculty of Biochemistry, Biophysics, and Biotechnology (currently 4 students) 2. Research a. import and maintenance of in-house compounds databases b. prediction of some physico-chemicals properties c. visualization, presentation

I would like to use this software for the design of some heterocyclic compound library which will be further used for fragment-based virtual screening. We will use the softer ware to draw chemical fragments, linkers, and functional groups for the further enumeration of chemical library. After transfering the format to SMILES, we will further use other software for enumeration of the combinatorial library.

Wahlkurs: Computerunterstützte Chemie-Experimente Multimediatechnik soll eingesetzt werden: Erkenntnisprozess am Bildschirm fördern, mit effizienter und anschauliche Darstellung von Versuchsergebnissen. Erläuterung von Grundlagen zum Verständnis chemischer Experimente. Ermittlung und Interpretation von Ergebnissen: Modellierungen, Auswertungen, Daten, Bilder und Sicherung zur späteren Wiederverwendung. Molekülmodelle von Experimenten: Versuchsvorbereitung und -auswertungen anhand von Bildern

To make the structures of the organic compounds

Researching reaction mechanisms of catalytic dehydratio0n/decarboxylation of lignocellulosic bio-oil to bio fuel

Teaching molecular modelling, organic chemistry and chemical informatics.

Looking and creating small mol. structures

using for teachprograms.

I am teaching \”Introduction to Computer Science II\” in the department of applied chemistry. One of the course object is that students of appled chemistry should know how to publish interactive 2D chemical structure on WWW. I found that \”MarvinSketch, MarvinView and MarvinSpace applets\” are more powerful than Chime plugin, therefore I am going to use \”MarvinView applets\” instead of the Chime plugin this year.

To illustrate the reaction mechanisms and simulate them. To calculate the charge distributions of molecules and photochemical properties.

teach kids

HPLC separation science molecular interactions

I\’m working on porous materials, which have several typical networks. I can use this software to build up and view a model. I also plan to use it for my teaching.

I am using the software to model dendrimers both in teaching and my research.

My major research is quantitative structure properties/activities relationship. Molecular and atomic properties are required to make prediction model. Marvin is quite good free software and very useful for my research and publications.

We will use the for QSAR study,Virtual Screening,Drug Design ,Establishment of a database.

Educational aims (pharmacy) –> drug absorption, drug kinetics

To study the SAR of the compound we designed and separated.

the aim is pka prediction by semi empirical tools, i will use this software to do conformational analysis for the structure i want to calculate

Our gruop trying to explain the mechanism of the of the voltage-gated sodium channel blockers.We found that these drugs can be divide at least two large group by their effect to the channel gating kinetics.We executed electrophysiological experiments on 3 different pH, and want to calculate the logD, pKa, isoelectric point of these drugs, to explain the changed effect on different pH.

I am evaluating this software to determine whether or not it would be suitable for introductory college chemistry students to use it to draw and visualize 2D/3D structures of molecules, including isomerism in organic molecules. I am also working to develop activities where students can use some of the calculator features (log P/D, protonation) to connect the structure and what they know about bond polarities and intermolecular forces with drug design considerations.

Modeling of surface groups of carbon adsorbents to predict their properties and establish most realistic structure.

Superpose small molecule Calculate chemoinformatics variables Optimize molecule structure 3D visualization

We use these kinds of programs to draw chemical structures, to energy-minimise them for docking to protein structures, and for presentation purposes. When we use your software to do so, we will cite the software.

The software will be used for teaching in Chemistry Olympiad courses offered by Allameh high school.

Teaching: provide students in physical chemistry inexpensive software for preparing chemical structures for analysis. Research: molecular sketches for research articles and text-book I am writing.

Teaching undergraduate chemistry and biology courses

we are in the research of metabolomics and metabonomics and set up a database of ingerated the chemical material

I\’m teaching Molecular Modeling and Software applied for chemistry and Biochemistry

i am working on plp project for that i need this software

This will be used for study and research performed in my Organic Chemistry lecture and lab courses. It will be used to draw molecules for use in homework assignments and lab reports. It will also be used to understand the concepts of reactions, molecule formation, and structure.

Calculation of polarizabilities of small molecules

for a project of the university I need to know some information about Befunolol and his receptor, with the Marvin Sketch I will know a lot about this medicin.

We use the software to show undergraduate students molecules. Since we are in the physics department, it is an easy way to explain chemical symbols and how they relate to structure.

I plan on using the software as a curriculum evaluation tool and proficiency yardstick and feel it would be invaluable in planning more cohesive course outlines than we are presently able to do. Being an integrated package it would allow a more complete front-to-back overall approach than we are currently able to manage. After an admittedly too short a \”test\” I further think it allows in depth analysis unavailable with any tools we currently have at our disposal, and will increase the overall proficiency of both students and tutors.

Teaching/Basic course in toxicology

the program will used in my PHD work to caulcule the conformation of same macromolecules and this cauculations will be used as a base form cauculations of molecular bonding energy. The main objective is explain the molecular energy dependences on the molecular interation to explain de unordered natures of the polymeric materials.

Our research is about the MAP kinase p38. I search for new ligands, called the Suberones. I need JChem for implementing algorithms for De novo design, fragmentation of the present synthesized structures, looking about the fragments an build new potential inhibitors for the p38 and so on.

NMR investigation of small heterocycles and bicyclic compound Dynamic NMR Computer and Internet Technology Programs for automatic collect and processing of NMR spectra Spectral databases

My interests are calculating pKa with marvinsketch to determine the acidity of additives to be used in peptide chemistry

Had gotten a licenses for this software last year. While rebuidling a new image for our 2008 fall semester I noticed that the licenses will expire on 9-1-2008. I will note that I did download and install the newer versions of the software that are available on the chemaxon website. This software is used for teaching students in our bio chem departments. Please let me know the new license information. Thank you Ryan Vega

\”Introduction to Chemoinformatics\” course was adapted from an undergraduate course of Chemoinformatics at the Seoul National University, Korea. Each session included a theoretical presentation and a practical session. The practical sessions of the course were mounted on the basis of software freely available to students, as well as public data sets and web services. All required resources are available from links at this web site, enabling students to study and practice autonomously either at the practical sessions and after classes. We need ChemAxon Packages to teaching practical session absolutly.

We teach ligand-receptor interaction We study interactions in general

Redaction of handouts. Introduction with students to the structure of organic compounds. Working in collaboration with one of my colleague who did already subscribes to you Academic Package license.

drawing of molecules for scientific publications and teaching (overhead presentations, lecture notes, exams…)

elucidate pharmacophore of Ribonuclease A

chemical biology/re-design of enzyme active sites/divergent evolution of protein function/protein engineering Im constructing a library of ligands in order to reconstruct aminoacid positions in different active sites to rach new enzymatic functions

Crystallography of proteins with small molecule ligands

We are performing experiments to come to a better understanding of the solubility behaviour of poorly water soluble drugs. We are collecting a series of physicochemical properties in advance and in order to obtain a reproducible data set, we a currently seeking for a good software package to determine properties such as log P, log D, pKA, number of rotatable bonds, H-donors and acceptors.

Teaching of postgraduate students in PhD studies concerning molecular pharmacology and analytical pharmacology Teaching undergraduate students in understanding pharmacological principles

The software packages of chemaxon are an excellent chemoinformatics program for chemists. We would like to obtain an academic copy for our research. Nowdays, our work interests are focusing on the discover of high potent and selective inhibitors of kinase by computer-aided drug design methods.

School of pharmacy: medicinal chemistry

Estimation of pKa and LogP values mainly for supramolecular chemistry design purposes.

Natural product chemistry

We would like to study the biological activity of the newly synthesized organic molecules and we want to correlate their activity based on their properties such as pKa. This will allow us to design or modify the compounds based on the activity of the compounds and their properties.

Dear ChemAxon, I would like the license for this product because will be used by my brother that is an undergraduate student as support of his chemistry studies. many thanks for it, Damiano Portinari

I will use it for drawing structures and conformational analysis.

using it to demonstrate structures and concepts to students that i tutor also using it to draw and name structures i\’m using in my honours research

We use this software to demonstrate the molecular dynamics studies of few small molecules to the students.

Studying the adsorption and permeability of dissociated molecules particularly dyes and fluorophores through the biological and synthetic membranes.

Jchem,Marvin products will be very much useful to carry out our research and provide demonstrations for the M.Sc Bioinformatics students in the field of structural Bioinformatics.

Project involves molecular modeling of membrane protein bound to a ligand. Marvin will be used to model the ligand.

conformations analysis

The research involves chemoinformatic and molecular modelling applications in the following fields: -drug design and targeted therapy. -enantioselective recognition and separation of racemates. -stability of organic compounds

To teach mechanisms in organic chemistry.

I want to predict the possible metabolite site of a target molecule. I think the solvent accessible surface provided by marvin would satify my need. i like it!

Analysis/desig of ligands to bind in newly designed active sites

We would like to see how useful this software would be for teaching students to draw structure for their lab reports and we would like to use this for drawing our own structures for research purposes.

I am a Student of Freiherr-vom-Stein-Schule (school, where I make a Workgroup for jounger students in the naturale subjects(Biology,Chemic,Physiks)

Properties od Materials in Chemistry and Physics

I\’m working on molecules organization

i request this programm for a better study of chemistry.

About CB2 receptor ligand screening

To create and visualize gaussian input/output files.

Standartization of compounds and storage of database of different compounds we are working with. Calculations of aromatic bonds in compounds. May be, calculations of some properties (in future & if available).

chemistry

I design new chemical compounds and your software is very useful for recognition IUPAC Names.

My subject is Crystallographic Computing and I need a program (running on linux system) to build molecules to import in my program.

I am a PhD student at TU-Delft located in the Netherlands and my advisor is Professor Gary Amy and co-promoter is Professor Hans van Dijk. I would like to use this software to calculate the number of double or ring structure to compare with the model called BIOWIN (US EPA) which is the model to predict the biodegradability (QSBR). I am trying to find all physical chemical properties if there is any correlations between the biodegradability and the phsical chemical propeties. I believe there are some connection such as aromatic structure won\’t degrade as much as aliphatic structure. I also MW might be relate as well. I have run 160 chemical compounds with BIOWIN and I am trying to corrlate with physical-chemical properties of the chemicals, especially in topology. It is very diffcult to find the number of each ring and different types of bonds for 160 compounds. Please allow me to use this software and of course I am going to put the reference in my paper. Thanks!

doing project on qsar analysis and required for calculation of some critical descriptors

I am gonna teach molecular modeling.

I\’m involved in a virtual screening protocol development in my PhD studies. I\’m intersted to use a your product to my studies.

Using this software we will design and screen out various molecules as potential leads in common diseases, just as a acedemic research (but not as a commercial research) in the feild of medicinal chemistry. our major emphasis will be on structure-based drug design and to some extant on ligand-based drug design.

Studying the permeability of ionizable and non-ionizable compounds through biological and synthetic membranes and constructing models to predict their peremeabiltiy using pKa, LogP and LogD values.

Examining Metabolite structures.

Both project and teaching is involved with drug design by molecular modeling that have to use MarvinSketch for predict the structure and thr properties of each compound.

To show live demonstrations of chemical structure and properties during undergrad Chemistry course lectures.

I am looking at downloading a sample of the academic software for chemistry to screen it for suitability for use in secondary schools in PNG. Thank you. If the curriculum team approve the software, it will be used in computer labs in schools. At present there is no viable internet access for the vast majority of schools in PNG.

We would like to use KCluster package for clustering a database of compounds and perform shape matching VS. We are working on virtual screening for finding novel AIDS entry inhibitors.

I will be using this software as an aid for student to master the intricacies of organic structure drawing, nomenclature, and 3D visualization.

Evotec is currently sponsoring me to do a part-time PhD at the University of the West of England (UWE) in de novo molecule design. I am looking to use a number of the Chemaxon tools, but in particular the pharmacophore descriptor tools as a fitness function for the de novo generation algorithm. The research involves looking at evolutionary techniques (GA and EP) but more recently investigating the use of software agents for molecule design.

Preparing exams, work sheets, handouts and posts to put on my website, fbanks.info. I may promote it to students if it is good. When I know what the software can do I might be able to add other uses.

The dissociation mechanism of small molecules analyzed by Mass spectrometry

My research involves studies of molecular interaction with biomolecule. I would like to try this software for visualizing those interaction in the 3D spaces.

Teaching Chemoinfromatics applications for pharmacy students. Molecular models, properties calculations, database search, generation and application. Research: Property calculation of potential synthetic targets, database search and construction for new antitumor compounds.

- teach grad. students ab-initio techniques research on organic semiconductors

General drug discovery applications with respect to the development of antimicrobial peptides as therapeutic agents

Molecular modeling, partition coefficients, polarizability

By far my interesting is only on the organic reaction pathway and trying to evaluate the Reactor in your products.

organic chemistry, medical chemistry.

antioxident in polymer.

I am beginning lab work in organic chemistry and therefore need software to be able to create research and documentation papers. Of course, your software will also be helpful – and probably indispensable – for the further course of my studies. For my lab work I mostly need to be able to create chemical structures of molecules, which I can\’t find as freeware for my Mac, but a database and advanced simulation software could make things a lot easier for me, too.

Quantitative Structure Activity Relationship with cationic lipids as DNA delivery reagents : how to make sense with so far obtained results and to establish a guide for future syntheses.

Testing purposes in generation and standardization of HTVS libraries in the Fight AIDS@Home project.

QSBR of ionic liquids

Using new media possibilities in chemistry teaching.

study reaction of polimer

I am working in structural bioinformatics and i will be in need of generating lots of conformers of the small moleulces and working in the dynamics and soem cheminformatics works too. so the tool form chemaxon will be of useful to my research work.

The program will be used to draw structures for the practical course in organic synthesis.

ENVIRONMENTAL SOIL CHEMISTRY, SOIL SCIENCE 321 AND SOIL CHEMISTRY, SOIL SCIENCE 621 PREDICTION OF ENVIRONMENTAL PROPERTIES FROM MOLECULAR STRUCTURE.

MODELLING OF VIRAL PROTEINS FOR MODELLING OF PEPTIDE EPITOPES

Fo Doing research and teaching in the field of medicinal chemistry

The molecular foundry at Lawrence Berkeley National Laboratory serves as a user facility to train visiting scientists, post-doctoral fellows, graduate students and undergraduates to use our facilities and know how to conduct cutting edge research in nanoscience. Many vendors consider our facility an acadamic institution for licensing and pricing. Please let me know if we will qualify for your program. For additional details on our facility and program please see our site at foundry.lbl.gov

To calculate logP, logD, pKa to predict ADMET properties

teaching of Organic Chemistry for about 30 students

The anticipated use is generation of small molecule conformations for simulation of binding to viral particles. Additional uses may include maintenance of departmental compound libraries (database-driven smiles string matching), as well as standardization of structures and preparation for simulations (charge assignment, tautomerization, etc.).

teaching structural biochemistry for student nivel baccalaureat STLBGB . academic site in the future .

design and synthesis of nucleoside dereivatives as potential antibacterials (inhibitors of aminoacyl-tRNA synthetase enzymes)

Entering compounds into database

Theoretical description of the tautomeric equilibrium primarily in the gas phase.

for the complete advancement of students through chemistry

Chemistry of boronic species and uses of them in Cross Coupling Reaction.

Hello, I am currently in the process of assembling a small library of molecules that modulate lipid bilayer material properties. Then I am going to see I can find a QSAR between my molecules and their membrane modifying properties. I am hoping that I can use you’re software to help me create and manage the compound library, maybe even generate the descriptors though you’re Calculator Plugins. Thanks, - Helgi

The software shall be used for performing certain tasks of chemoinformatics.

visualisation of chemical structures

create a chemical database for research, for student draw the molecules and stock them in the database, especially for searching the existence of substructure of a molecule with Jchembase, and then we want to create a database for spectral of molecules,too

I am working as a TA for a pharmacoinformatic class. I found this software on the web and think it will be great help to explain the structure and other physical chemistry property during the class.

Virtual Screening for LpxC through \”Basic Patch\”

Bioinformatics course in the Department of Pharmacy

Molecular structure databases of drugs and new substances of pharmacological interest. Web-based eLearning systems for the students of the University of Vienna. Illustration of the possibilities of the geometry optimization, conformational analysis etc.

I will be using the software in order to get a better understand of the chemical structures of the compounds I will be looking at (I.E. 3-D).

Klustering & virtual screening

Analysis of redox and repair inhibitors of a dna repair protein we are studying for basic science studies. Would like to find additional molecules for academic analysis.

Virtual drug screening

I am doing a study into the reaction rates of different amines with complex imidates as part of my PhD research. I would like to be able to use the software to estimate the pka\’s of some of the amines I am interested in, in order to observe any trends with the experimental data obtained.

Plan to use ChemAxon tools and calculators as a resource in MEDCHEM 635, a special topics course for Drug Design. In particular I will be giving lectures on the strategies and tactics of Lead Discovery and SAR analysis, where the calculated properties of compounds will be higlighted. Enumeration/fragmentation and fragment analysis may also be incoporated if possible. For research, an investigation of the chemical properties of known drugs deconstructed by therepeutic area and/or gene family is planned.

we appreciate your offering these great software free to use. we use the software to build molecule model, to draw the result and in the future, we hope to do drug simulation

I have developed a novel in silico screening technique, but I need to do additional searches (Markush,etc.).

use in conjunction with chemical inventory for health and safety purposes at the Unviersity of Kent/Department of Biosciences JChem JAVA library and the Marvin applets

To study some protein ligand binding structures

Shearch of the lowest energy conformation of a oligomer chain and of a supramolecular oligomer-fullerene or oligomer-Carbon Nanotube system.

We are testing software to visualize, calculate structures and analyse molecules studied also by NMR

I would like to use the program to calculate physical-chemical properties in some QSAR studies.

Our research group work in the field of computer-aided drug design inside the \”Universidad Central de Las Villas\”. We use both ligand and structure-based drug design tools for the prediction of several pharmacological properties, as well as in the research of new leads compounds with various biological activities. We plan to use JChem for the management of databases, properties calculations, pka calculations, protonation states asigment and several tasks needed during the drug design process. ChemAxon software will be a very good alternative to the very expensive commercial softwares to which we have no access since, although having more than 150 publications in the WOS journals our financial support is limited.

Teaching basic inorganic chemistry. Teaching pKa concept of organic acids and humic substance.

Molecular modeling group: Docking, MD, HTVS. All the fields of Computational chemistry aimed to understand and help the Drug design process.

This software will be used to generate tables of lead compounds in an SDF format from a high throughput screen.

use in ligand receptor research

The study of molecules conformations helps us to understand some spectroscopic features, for example, multiplets in the 1H NMR spectra. The ChemAxon\’s software will be use in the generation of conformers for flexible organic molecules.

I\’d like to view viewing lipid structures with sdf files with the general aim of developing tools for lipidomics research

This software will let us to understand the chemical structure of many small molecules which are potentail candidates for a binding with a specific receptor.

for a presentation

Research in pka valeus of medicine in interest

Probe discovery and medicinal chemistry

Software will be used both in class (15 students) at advanced level, master student thesises and original research work. We will use software for descriptor analysis, such as estimating pka for groups of ligands and for visualisation.

Creation of web based databse and interface.

isomers structure

To draw derivatized dye molecules used as photoalignment layers for liquid crystal devices.

we are synthesizing new chemical entities and checking their activities. now we plan to do qsar 7 molecular modelling of compounds. thats why I need it.

For making a database containing the details about the volatile oils present in black pepper and to display the structures and their conformation of the compounds in the essential oil of black pepper. I want to know the pk values and all about the structure.

The scholl parcipates to NJ chemistry Olympiads. One of the events requires building molecules from scrathc followed by energy minimization. Aother application will be searchong for the most stable conformer in cis-trans isomers.

These tools will be used to develop and include 3D images of chemical compounds not just static but in movement, for the courses of organic chemistry and pharmacognosy.

I would like to use this software to determine bond distances between atoms in various types of molecules. This information will be used to estimate the number of molecules capable of fitting in the hollow core of a protein scaffold that could potentially be used for drug delivery applications.

Research of the atmospheric degradation of aromatic hydrocarbons

Library diversity assesment, QSAR model development, and virtual screening. No current implementation aims. New to ChemAxon products.

pharmacophore development and comparison with potential molecules with activity and affinity to specific biological targets

I will use this to calculate phys chem properties and to show certain properties of molecules

Wish to use Marvin to generate conformers of small molecules and peptides.

I will first evaluate the softwares for teaching and I will then extend to students and, maybe for research

The software will be evaluated for use in a number of courses and for research. ChemDraw is currently used as individual licenses for research publications. The Department will evaluate available software for use in the curriculum.

The programs will be used for visualisation and generation of descriptors for medicinal molecules in the course of generating QSAR models for predicting bioactivity and ADME-properties

modified bases molecular dynamics simulation. Charge and electronegativity calculations of modified bases

Basically, students of the 7th to10th high school grade are very interested in scientific lessons. However, this reverses during the higher secondary I level, especially in chemistry and physics. At this time, a great portion of the pupils turn away from chemistry and physics. Because of the abstract content and lack of naturalistic teaching, most of them sense lessons in chemistry and physics as too difficult to understand. Since both, boys and girls, deny scientific education in an equal degree, there will be no real explanation for this global rejection. Consequently, most students decide against taking advanced courses in chemistry or physics in the secondary II level because of the fact that chemistry and physics still have the reputation that the educational topics that are dealt with in these subjects are only for experts or a small amount of gifted students. Through this electoral behaviour many students make far reaching vocational choices: Appealing professional fields of so-called \”hard\” science and technology” will usually not be considered. NAWI lessons offer a possible stage or platform to change this general attitude of many students. The most important part of the NAWI tuition is the teacher, who has to show a high level of personal commitment because he/ she has to impart knowledge (the content of the lessons) and encourage the motivation of the students. If you are interestet in our investigations, you can send me an email then i\’ll give you a short document (3-4 pages) that discripes our projects, aims and results

We are analyzing the effect of special cytochrome p450 enzymes on various diseases. So the metabolizing of special substrates which also can act as competetive inhibitors are studied. In silico determination of these interactions would be first clues for further investigations

generation of 3-D instructional video for steochemistry and conformation lectures

Green Agrochemicals

My research is on the developpment of pesticides analysis

I am a young scientist recently appointed to the chemistry department of the university autonomous of barcelona. My main research theme is the study of protein-ligand interactions for drug design purposes. I\’ll use marvin in my day to day work for analysis ligand main chemical properties. I also plan to use marvin in order to add ligand based analysis to my own research, something that I presently lack (I have been formed to structure based drug design). On the teaching side, there is a lot of things I plan to do. In particular, I have been asked to generate different introductive master courses of medicinal chemistry for chemistry students. I think marvin fits perfectly my requirements.

In my dissertation in drug dicovery field, I need to manipulate small organic ligand for then submitted in MD and obtain binding affinity data.

To study organic cation transport in different pH

My project is looking at photochemical parameters for examining the efficacy of UV light as a treatment mechanism for removal of pharmaceuticals and hormones from drinking water. One important parameter in the efficacy of UV light for treatment is ability for each contaminant to absorb light. This is pH dependent if there is a protonation site within the chromophore. For these compounds, it is valuable to know the pKa. Although experimental measurements are being made for these compounds, I would like to include some pKa calculator values for comparison.

Basic chemoinformatics. SMILES language. Molecular modelling. Structural Biology

i am writing my bachelor thesis and need to convert moleculs in mol format to their corresponding iupac name. the goal is to check out the results of a fingertprint analysis of the structures.

I am an undergraduate Biochemistry student working with Professor Mark Meyerhoff in an attempt to develop thromboresistant NO releasing/generating polymers for biomedical sensor coatings. We are employing LbL construction techniques using various polyelectrolytes to immobilize compounds containing catalytic substrate on various polymers. I am NOT applying to download your software on behalf of my research professor or my department. I will be the only user and my intent in acquiring your application is mainly to be able to visualize various molecules (mainly organometallic compounds such as diselenide species) for my own information purpose while working on this project and to be able to access information such as pKa predictions using your various addons. I will only be using your software while working on my current research program described above in the coming months.

I would like to use this in an intro chem class over the summer. If it works out, we would work it into a main sequence course and be able to provide more details

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I graduated korea university with MS majoring in environmental soil science. I teach college students about general chemistry, analytical chemistry, etc.. I want to show chemistry structure and other chemical characteristics to college students. So I beg you to use this software.

Preparation small molecules for docking

We at lab do molecular simulation and virtual screening. Marvin space will be used to view the outcome and also to perform task such as log-P calculations.

As an organic chemistry instructor, I intend to use Marvin Sketch to produce structural formulas for use on exams and in classroom presentations that are aimed at teaching the reactions and reaction mechanisms for the common functional groups, IUPAC nomenclature, and the various forms of isomerism. If the software could be loaded on select computers for student use, it would allow students to further explore and test themselves on all of the concepts mentioned above. It is also expected that students could make extensive use of the software to produce very neat and easy to interpret structural formulas for inclusion in their lab reports.

I would like to research the kovats number index.

Calculating molecular properties (and its modifications) before performing actual CE experiments in order to determine optimal separation conditions thereby decreasing method development time.

Generation of 3D conformations of molecules, graphical representation of molecules and complexes, structural searching.

QSAR modelling, homology modelling and docking.

Organic Structure

Teaching organic and organometallic chemistry

Within the research project Virtual Library for Chemistry of the German National Library of Science and Technology in cooperation with the L3S reseach centre we are planing to use Chemaxon tools for - storing and retrieving chemical data with JChem Base - using Marvin as the user interface for structure searching and display of query results. Modules developed in this research project will be implemented in the german chemistry portal http://www.chem.de later on. Further information may be found at: http://www.l3s.de/vifachem/

We would like to evaluate your tools for QSAR research on membrane transport. Predicitve toxicology is also taught to some extent at our university.

Aim: to show the shape and the 3d structure of molecules to nurses during seminary. Thanks

Wish to use in teaching medicinal chemistry, other I need for searching for the most stable conformers, and predict stable form in develop chromatography.

We want to use the database function to record chemical structure and viral inhibition results for a growing library of small molecules. The SAR will be correlated to produce pharmacophore models through combination with other modeling packages. Of particular interest is development of effective treatments for currently drug resistant infections.

A de novo design tool using KNIME. Marvin will be used to visualise molecules and reactions and the calculator plugin will be used to calculate properties such as LogP.

We are looking at the physiochemical properties of several essential oils to determine the reasons for their variance in antifungal abilites.

Polymer Modification for pharmaceutical uses

We are currently developing an artificial chemistry that uses models of real atoms in order to obtain clues about the origin of life.

Primarily interested in pKa values.

Currently, we teach a course in computational chemistry and drug design. We are implementing some QSAR strategies and would like to include Marvin a JChem in our course. We have approximately 270 students in each of the 4 years of the undergraduate degree course. We are hoping to include such things as homology modelling, and docking simulations as well as pharmacophore perception.

The software will be used in association with CHE 321-322 out sophomore organic chemistry course. We have and active discussion board and we want students to be able to post graphics from a convenient source. When implemented software access will be from the course website at: http://www.ic.sunysb.edu/Class/che322jl/

I\'m not really sure what I can do with this but feel it will be of great use in teaching our undergraduate students in the Pharmaceutical Chemistry degree. In research we use many different biophysical techniques. A building/visualisation tool will be of great general use.

Integration into small screening unit with the aim to drive chemical genetics research.

Our use of the JChem package will be mostly limited to the jcsearch program for SMILES comparison. We would like to test its ability for detecting relationships between PDB molecules and known drugs.

Learn to make a chemical database

I am entering my second year towards a Ph.D. and I will be required to be a teaching assistant for at least 2 courses of which I would like to implement ChemAxon software in some form yet to be determined as I am not yet aware of what courses I will T.A. for. I am expected to publish journal articles several times in the course of my Ph.D.; citations to software will be used if appropriate.

our lab focuses on finding and synthesizing small molecule probes to affect biological systems and disease mechanisms. We would like to use the academic package in our efforts to synthesize our hit compounds as well as compound libraries for high throughput screening

I load the drugs vincristine and topotecan to liposomes. I need to understand their protonation profile over the pH range 4-8 in order to do the discussion of the loading optimization in my Ph.D. thesis.

We have a med chem project running in our lab. We will primarily be using Instant JChem for maintaining a database of synthesized compounds with reactivity and toxicity information.

I am attempting to evaluate this software as a substitute for ChemBioOffice/ChemBioDraw as an aid to visualization of organic and biological chemistry.

For use in my study

I am teaching Organic Chemistry for college students. Programs such as Marvin Sketch will be very useful in teaching them chemical nomenclature and organic reactions. I am also part of the Natural Products Research Group of our institute where organic reactions of our studied compounds are necessary for publications and presentations of our research.

Analysis of marine lipophilic toxins in shellfish

QSAR descriptors and Molecular Modeling studies. Project(Thesis): QSAR study of clerodane diterpenes and their evaluation as potential inhibitors to the p53-MDM2 interaction.

I work on virtual screening for drug discovery using grid infrastructures. Taking into account the huge amount of data to analyse, I would like to use your tools for my post-processing analysis to cluster thousand of compounds and extract chemical features. Your software will be an added value for our data analysis. Moreover your tools will be used for databases preparation before the calculations.

I am working on Pharmacophore screening and also need to build databases for the same. I will be using it for my research activities.

To have estimates of physical constants/parameters of various molecular structures.

I am a organic chemistry student and need a good chem. suit.

preparation of structures for documents prepared for students

JChem will be used to store and query libraries of commercially available compounds

We are investigating the effects of purine-based drugs on ion channel activity. This software will be used to help us examine the molecular properties of compounds found to affect ion channel gating. This is a very new area of research for my lab and I am searching for a software package that is easy to understand, but sufficiently powerful to allow me to gain molecular insights to efficiently generate more potent analogs. We will be testing the drugs on voltage dependent calcium channels. Our recent paper in J. Neurochem (105:1450, 2008) was our first on drug structure-activity relationships.

Will be used to inspect structures and generate multiple conformers for ab initio optimisation.

JChem Base used for viewing/searching chemical databases.

Docking and Virtual screening

Synthetic Chemistry

Teaching - Use applets in class websites (through blackboard hopefully) to expose students to chemical structures (organic) and macromolecular structure (biochemistry). Also, the Marvin applications will be made available for students use in the Chemistry computer lab for outside class learning. Research - Interested in novel small-molecule ligand discovery using both pharmacophore modeling and structure based design and docking. Hope to use library enumeration, library file format conversion, and possible Instant JChem to store docking results.

I am looking into using chemaxon to organize experimental characterizations of chemical systems. I currently use ChemOffice, but aspects of it to be confusing. From the description of the database capabilities of chemaxon I think it will be a better fit for my needs

we use it for chemical clustering and similarity search with database building.

Evaluation as a multiplatform (windows/linux/mac) alternative to traditional chemistry sketching tools (chemdraw, isisdraw..). Initially it will be intended only for personal usage, if the application is found satisfactory it will be introduced to other users to poll their opinion.

http://www.sgc.utoronto.ca/SGC-WebPages/sgc-toronto.php

As a student it is absolutly necessary to have a powerful tool to include chemical structures in presentations, papers and protocols.

Infrared Specctroscopy of complex compounds at very low temperature

For personal use in projects, reports and presentations. i hope to share with my peers my experiences of using this programme.

To discover new chemical space by creating natural product like combinatorial libraries that will aid in the discovery of chemical probes to study cellular pathways.

I plan to use this program to draw structures and view them as 3d models.

I would like to use your software to teach basic concepts of molecular modelling including physiology based pharmacokinetic modelling at our university. In order to estimate pharmacokinetic properties of chemicals, students will have to perform physicochemical calculations for the compounds of interest.

Investigation of the monomers and conductive polymers properties.

identifying the novel substrate of enzyme

currently I am undertaking my external placement as an affiliate graduate student in UCSD and particularly in Phi Bourne\'s group. I need this software package to measure some chemical properties of drugs, like the logP and logD values.

I am working on the reactivity of organic molecules on surfaces. The software will give me a first step in the calculation of the molecules structure and atomic charges. I also teach atomistic and molecular structure at the university, the software will help me for redaction of exercises for students.

I need the Java API that takes in a SMILES string and returns various properties of the compound. Right now our immediate need is to calculate the logP values for all compounds in our database but we will also need it in future to calculate values like Pka, logD, Molecular formula, molecular weight, structure, etc. of any given compound.

We intend to use JChem Fragmenter to create fragments from ligands in the PDB to test against their corresponding targets using a novel flexible docking method developed in our laboratory. We also intend to use JChem Reactor with the new flexible docking method to experiment with new combinatorial and rational methods of building potential drug leads. The final aim would be a new fragment-based structural design technique.

I am trying to use this as a more portable, platform independent drawing program to replace currently used programs (chemdraw, etc,). I am using it for reaction mapping, structure tables, and meetings.

QM/MM calculation molecularf dynamics

research structure and function of insulin-like molecules. I chemically produce these molecules including natural and non-natural amino acids and analyze the 3D-structure by NMR. For this purpose I would like to use the MarvinSketch option to produce non-natural amino acids for deposition in the protein databank

For research tool and teach computational chemistry

Modifications of drugs from their database form to their biologically active form.

MICROFLUIDICS AND NANOFLUIDICS

Structure to smiles, calculation of pka and logP. Structure drawing.

I am using Genetic Algorithms to try and predict docking scores for HIV tar, I use small molecule descriptors as the values in my Genetic Algorithm.

Our study is about mechanism of interaction between protein and organic compound. We perform the site-directed mutagenesis of protein. So we want to know the molecular surface of amino acid, and use this software to try to explain our results of study.

Determining chemical and physical properties of small organic compounds that act as calcium channel blockers in platelets.

We implemented virtual screening to select inhibitors of Protein-Protein Interactions. During the post-screening period, chemical diversity analysis is necessary. So the JKlustor in JChem Base package is desirable for us. Thank you for your support.

Chemical compounds database managment, property prediction, clustering

Protein modification with hypochlorite modified lipids

Evaluating for use in final year courses in application of computational chemistry and rational drug design

Teaching of organic and/or medicinal chemistry to students.

Study of chemical compounds

Structure Drawing in the discussion section in order to make my presentation clear.

Please pardon it though there might be a strange expression because it uses the machine translation. I am researching concerning the synthesis of the new extraction reagent. An appropriate design of experiment is expected to be able to be constructed by requesting a value calculating chemical before chemical physical properties of the new extraction reagent (for example, logP and pKa) are measured.

Here, in our lab we are doing the lead identification and virtual screening studies for some potential targets. The main startegy which we follow is QSAR.

Software will be used to complement our structure based drug discovery program to identify novel target ligands.

Computer Aided Dug Design

Course in computer-aided molecular design (further details on http://www.uibk.ac.at/pharmazie/phchem/camd/staff/wolber.html and http://orawww.uibk.ac.at/public_prod/owa/lfuonline_lv.home?open_in=search&sx_in=&sy_in=&c_in=3&sem_id_in=08S&suche_in=wolber&opened=e0eE Teaching aims: teach pharmacists basics of cheminformatics and modeling.

Relationship between molecular structures and LC-MS properties of analytes

We teach general chemistry for pre-university students and university students in their first or second year studing general chemistry, introduction to inorganic chemistry, introduction to organic chemistry.

for teaching implementation

Drug design

Need to calculate pKa values and other parameters of compounds we use to do neuroscience research

Creating a database of molecules for recording data from biological assays.

Cheminformatics & Computational Chemistry research. Calculations of molecular similarities and physicochemical properties, enumeration of chemical libraries, storage and retrieval of chemical structure collections, etc.

Try to evaluate the applicability of the tool on the study of metabolic pathway completion and study the evolution of pathways.

Getting molecule properties from structural information.

We will use the software for students who choose medicinal chemistry a main focus during their study. Drug candidates which are examined in the work group will be used as model compounds for the calculations with chemaxon software to check if the molecules are compliant with Lipinski\'s rule of five...

Trying to determine Log D values of theoretical compounds in order to determine the range of compounds to synthesize to test in vivo.

I am a student and need a chemical drawing software that can also perform some calculations.

This software will be implemented through the BlackBoard Virtual Learning Environment and made available to those students registered on the MChem One-Year Placement Distance Learning Course which will be offered to third year students from 2009.

Veranschaulichung chemischer Moleküle

used to sketch small organic molecules for use in docking applications

use

To predict the physical property of chemicals and manage chemical databases

We teaching engineering chemistry for engg. students. also doing for chemical engineering graduates, organic chemistry, physical chemistry, analytical chemistry. I am working in the field of Liquid Crystals

3D structure visualization

Academic research in organic chemistry (synthesis of azaheterocycles)

at present I am working on proteomics.my work includes the evaluation of an antigenic protein for vaccine and drug target studies. for the data analysis I use multiple biological tools and for drug docking most of the tools require 3D structure or pdb file format which makes analysis complicated because pdb files for all the drugs are not present in the database. for this reason i was looking for such softwares which can import the 2D structure of the ligands and can convert them into 3D /pdb format.

Drug discovery, chemical data mining, chemical software development

Software is basically used for the Prediction of AMDE properties.

Mainly for search and simulation of chemical reaction

Research interests are in the computer-aided drug design, applied to identification of MMP inhibitors, caspase inhibitors and protein-protein interaction inhibitors. Virtual screening campaign and other drug design approaches will be applied. Your software would be very useful for molecules construction, properties evaluation and database managing. I didn\'t produced any publication so far as I have been working out of University, where I came back just few month ago. So I kindly ask you to give me the opportunity of using your software. Thanks in advance

I want the students to use the software for a lab where they determine what physical properties best correlate with melting point. I saw that this free software will allow for calculation of surface area and polarizability. In lab I have the students list a number of properties and after determining melting point we see which properties best correlate. Since this is a first time for melting point determination, many students are surprised that molecular weight has nothing to do with MP and number of H-bond donor and acceptor sites is most correlated.

Software will be used to view molecules within my classes. I also intend to use marvin sketch to draw 2D-molecules for use in my presentations and tu print on worksheets. Next step would be to use the software on PCs in classroom for students to draw molecules an structures.

tutoring 1st and 2 nd year students

The software will be used to calculate the phramacokinetic properties of small molecules.

Charge transfer effect in surface enhanced Raman spectroscopy

Evaluating for use in organic chemistry class and lab.

My research involves the calculation of ligand-protein binding affinities from force field-based simulation. I have to work with a variety of drug-like compounds and currently am mainly interested in your software for PkA prediction.

My research interest is focused on studying of Interplay between structural, physical, and chemical properties of chemically modified carbon allotrope (carbon nanotubes, graphene, nano diamond, etc.) for constructing new smart composite materials. My few resent publications are listed below. 1. Functionalized graphene sheets for polymer nanocomposites. Nature Nanotechnology, 3(6), 327-331(2008). 2. Preparation and characterization of graphene oxide-based paper. Nature, 448, 457-460 (2007). 3. Synthesis of Graphene-based Nanoplatelets via Chemical Reduction of Exfoliated Graphite Oxide. Carbon, 45(7), 1558-1565 (2007). 4. Graphene-based composite materials. Nature, 442(7100), 282-286 (2006).

To look for a better substructure search on on line website METLIN. To be able to view structures with more options and better speed. To data mine the database for metabolomics research. *Finding pathway maps simlaritys *In-silco discovery of new possible metebolites

Research: Origin of Life, prebiotic chemistry, protocell synthesis, synthetic biology Teaching: Biochemistry, Synthetic Biology

My work is in the field of nanotechnology. chemical modificationa and bioconjugation

estudiantes demo

For predicting various physicochemical parameters of steroid,piperazine,isosorbide based derivatives

Estimation of pKa functionality for chemical synthesis

We are currently working on visualizing HIV protein crystal structures to better understand mutations.

toxic compound database and predicting toxic compounds

Organic Chemistry coursework teaching.

To be used alongside other software applications in \"CHEM 305 - Computer Applications in Chemistry\' course.

Study of QSAR descriptors, Molecular modeling introduction and molecular shape analysis

Design of small molecule protease inhibitors

Synthesis of olanzapine analogues

Structure activity relationshiop of a new class of intercalating agents

I want to use the package to identify chemical compounds that could help stabilize proteins to get new protein crystals and structures using Xray-crystallography. It will be used internally for research here at the Karolinska Institute.

software to manage chemical libraries, to analyse In vitro Screening data; development of new methods to do virtual screening ChemAxon Tools were used especially by a student of mine, Samia Aci who has left the laboratory. The Academic license was under her name, and I would like to go on the work to finish it and especially to write articles about it.

The software will be used for presentation of chemical structures during my course of NMR spectroscopy.

To calculate log P of ionic liquids.

To teach basic principles of molecular dynamics

I am going to use the products to assist me in doing papers, visualizing chemical compounds, and better understanding in physicochemical and physical principles of drug actions.

Within the context of a virtual screening project, I would like to test the protonation state prediction routine of Marvin. In addition, as I recently heard about Marvin, I would like to try it, because I think it would be useful for other tasks in my research activity.

For designing combinatorial Libraries of G-protein coupled receptors. This will be for use in virtual screening experiments and later organic synthesis of selected hits will be possible.

Chemical database search and management Simple chemical structure manipulation Virtual screening Writing custom chemical informatics applications for in house use Computation of molecular properties like pKa, logP, etc. Depiction of chemical structures

The package will be used to generate images used in a course on molecular biology and genetics of prokaryotes

I\'m a college student in indonesia, i\'m not researching, i use this applications for studying

I really like the MarvinSketch and MarvinView 3D for making visualizations of molecules that we work with in our organic electronics research group. I am asking for the license because I want to try out the conformation plug-in.

Organic synthesization

research of new drugs

to use group plugins for the study of various organic molecules.

the understanding of distribution of charges of resonance.

molecular modeling

We develop new compounds with dual activity towards serotonin receptors, thus possesing antidepressant properties.

This license request is for using the mview and msketch tools by Prof. Peter Johnson\'s and Dr. Colin Fishwick\'s joint research group at the University of Leeds, UK.

I am a student of doctoral in chemistry e I would like to use in my research. I am studing medicine\'s electrochemistry.

I need to be able to do the problems assigned to me through AceOrganic... the plugin is needed.

naming of chemical structure by IUPAC for academic publication in international journals

didactics of chemistry

We are a basic research institution conducting research on mouse odorant receptors. We are in the process of screening panels of candidate ligands for GFP-tagged receptors in native tissue, using electrophysiology and calcium imaging as our primary assays. We plan to use the software to draw chemical structures, make physical comparisions between the ligands, and hopefully implement some kind of rational strategy in potential ligand selection. We plan to use the software in two ways. First, we will use Marvin to prepare PowerPoint slides to display odorants for scientific presentations at international meetings and institute seminars. Second, we will use the program as a teaching tool to display structures to rotating students (undergraduates and graduates), as well as to postdocs that will be collaborating on the project.

We plan to use the software for drawing polyketide structures which will be displayed on our future database of modular polyketides.

drug discovery - design research

Will be using standardizer to remove counter ions from sdf files. This is necessary to import the structures into our screening database.

We will implement chemaxon tools for our research in supporting the chemical biology research at SGC.

Want to perform molecular clustering, fragmentation, descriptor based methods, etc

We are currently synthesizing a number of compounds for several collaborators and would like to keep track of our compounds as well as any data that is obtained by our collaborators for any of the compounds. We would also like to be able to calculate logP\'s and pKa\'s, etc., when needed. Any publications that come out of this work will reference ChemAxon.

I would like to use the software of ChemAxon in the classroom, showing existing resources, and above show a link between the content of the classroom with that used in the labour market. I believe that with the full license for the use of such software in the classroom, can improve further the interest of students in chemistry.

Analysis of small molecules (chemolibrery) for docking studies.

Illustrate pharmacologic treatment rationale with logP/LogD curves.

Teaching

I am interested in seeing if and how this software will assist our studies into the design and synthesis of organic molecules.

Pre-university chemistry teaching. Software is important for providing visualisation of organic chemical structures and mechanisms. Some biochemical structures also important - especially conformation/carbohydrates/peptides.

Sketcher, substructure and similarity research. IUPAC generation 3D coordinate computation

We intend to use ChemAxon to teach chemoinformatics. We are planning an one semester course about chemoinformatics. Our aim is to teach our students how to use ChemAxon and other tools to estimate molecule properties and to predict them.

Use Marvin for teachin Chemistry.

for studying of stereochemistry (drawing isomeres) and calculation pKa of organic molecules

we are interested in performing hts in kinase targets in combination with NMR experiments

I will use this program to study molecules. I think this programm is very good for calculating isomeric forms. I would be very happy if i get a free licence. Adrian Pritzius

academic purpose

Study about heteroatom chemistry

Computational medicinal chemistry

Virtual Screening. Structure-Activity Relationships.

I\'m a student in pharmacy, so I will mainly use the software to help me with my studies

Carbohydrate Chemistry

I am keen to try to use this software as an accessible advanced filter for compounds (lipinski etc) which are found in virtual screening trials.

bioinformatics database

Use in my PhD on self assembly of artificial DNA structures

calculate and research charged states of drug molecules and model permeability to cell permeability.

This program is used to help students be able to draw chemical structures and analyze them.

We are developing a prediction of migration time in capilary electrophoresis were the pKa is an important factor, so we need to caclulates pKas for a library.

In analytical and organic reactions

Structure based and ligand based drug design; ligands for GPCR targets; optimization and SAR analysis of in-house compounds libraries.

design of pharmacologically active compounds and chemical-physical properties prediction

Self-teaching. Self-update with chemistry softwares.

Introductory organic chemistry lecture and lab

I IMPLEMENTED RESEARCH TO USE THIS CHEMISTRY SOFTWARE FOR TEACH IN CHEMISTRY ABOUT ISOMERISM, ORGANIC CHEMISTRY PROPERTIES.

Neuropharmacolgy

I want to use it for drawing the chemical structures or the calculation of its pKa. The pKa is an very important chemical property for me to develop some methods so I should to predict it the time I choose the reagent. And I really want to use this software to calculate the strength of the bond or the radius of the molecular. These information will help me design me experiments.

* Would like to perform molecular clustering, fragmentation, etc * Try to utlize and study the functionality by researchers

I would like to use this in order to complete my chemistry homework.

The software will be used in a course on application of computer methods in Chemistry. Students will use the software to sketch molecular structures and store them in various formats (e.g. molfile, sdf, smiles and inchi) to introduce to the various methods for computer representation of molecular structures. In a topic on molecular modeling, the software will also be used to view 3d structure models and generate structural descriptors from the models. The descriptors will be used in the estimation of molecular properties (basic QSAR).

computer aided drug design

The package is to be used to improve instruction of protein conformation.

We are doing ligand and structure based design for Gamma-aminobutyric acid transport proteins (GABA, GAT1-GAT4) and would like to use Marvin and JChem to 1. enumerate screening candidate libraries 2. setting correct pH protonation states before virtual screening. 3. maintain our own library of available compounds

Draw structures and create databases

1 - Organic reactions mechanism for undergraduate students: need for a fast and easy chemical formulae drawing system and chemical reactions available on windows and linux operating systems. Automatic representations of tautomers and resonance structures are also useful. A first draft of the theoretical aspects of organic reactions mechanisms will be available during this year on the department\'s web page. 2 - Evaluation and prediction of chemical reactivity and biological activity - for master and PhD students. Application of topology and fast computation of characteristics like logP, polar surface, charge, etc.

I teach a molecular modelling course for chemistry majors. I intent to use Marvin software as a drawing tool. I am doing research in computational quantum chemistry and chemical bond and Marvin is very useful to draw the chemical structures and to help to interpret the optimized ones.

The software will be used as a teaching and research aid for our postgraduate students in the Division of Medicinal Chemistry & Structural Biology. Specifically, ChemAxon software will assist students in learning and implementing chemoinformatics methods.

Teach molecular modeling application in medicinal chemistry. Edit molecules and property calculations for research in several fields (anti-HIV-1 and anti-HDAC as the major fields).

I teach a Principles of Medicinal Chemistry course involving how physical chemical properties of organic functional groups influence ADMET. We discuss logP, logD, pKa etc. I will use these programs during lecture. For research we are developing analogs of the natural amino acids for incorporation into peptide hormone/neurotransmitters. We will use the programs for calculating physical chemical properties of our analogs for comparison to the natural amino acids. We wish to modify pKa and logP/logD of the peptides we are studying.

I\'m working as medicinal chemist, i.e. design and synthesis of new enzyme inhibitors

Teaching in secondary school. Creating models organic compounds of all kind for pupils to name and recognise .

Currently evaluating a number of Chemistry visualization programs for implementation in course taught and research conducted.

Biochemical engineering Biocatalysis Organic Chemistry Thermodynamics

Basic molecular visualization.

PhD on heterogeneous catalysts.

Evaluating for the possibility of using this software as a tool to draw molecules for publications and teaching slides.

Teaching: Computational drug design for pharmacy students Research: My doctoral work is mainly in the field of QSARs

The Chemaxon data will be used primarily for teaching. When teaching pharmacology to my students (my primary role at the Univeristy), information about structures is important to present, as well as chemical information such as partitioning and pKa. In my research (pharmacokinetics) I will need information about structures from time to time (eg, molecular weight, partitioning, pKa, and ionization) for development of analytical (HPLC) assays.

I am teaching environmental biochemistry course for students of our department. I want to teach students the ablility to sketch the small chemical molecule , view and manipulate 3D structure of protein and DNA. Also i want get the ability to calculte the pKa and other properties of environmental pollutants and construct a small database for them. I think this software package is a good choice for these purpose.

* teaching in physicochemical properties of the drugs or active compounds * research in correlation of the physicochemical properties of the pharmaceutical compounds with their transport across biological membrane (intestinal ephitelium or skin etc)

I have just started working on crystallography after 20+ years in superconductivity. This field is fairly new to me and I am currently evaluating software to be used in this new activity, with preference to multi-platform packages that run (also) under Mac OS X.

A number of cellular oxidation and reduction pathways rely on the relay of electrons between pairs of cysteines and seem to be controlled by the specificity of intra- and inter-protein interactions. Many enzymatic pathways describe a conserved thiol-disulfide exchange mechanism to transfer disulfide bonds between separate components of the cellular redox systems. In addition to these inter-protein transfer events, eukaryotic and prokaryotic pathways share mechanisms for disulfide-bond transfer between several pairs of cysteines within a single protein. For our research work, we focus on enzymes in which cysteines lie at the heart of the catalysis mechanism and on the oxidative folding process by which a protein recovers both its native disulfide bonds and its native structure.

The software will be used to teach students taking our drug design course to prepare/analyze ligands for subsequent docking/QSAR analysis. Personally I\'d like to evaluate the software for my own research in drug design.

Teaching: Generate structures - save as *.mol files Use these to generate SMILES and IUPAC Names Use these as input to Energy Minimizations using GAMESS or PCGAMESS Generate LogP, polarizability, Polar Surface area to correlate with TLC rf values Measure bond distances, angles and dihedrals No web site implementations are in progress now.

will be using them for organic chemistry classes on campus

Molecular structure determination by Nulcear Magnetic Resonance Spectroscopy

I just want to use your software to draw the structures for my PhD thesis.

My lab is interested in the anti-diabetic activity of naturally-occurring molecules (such as flavonoids). I require software that will allow me to predict pKa, LogP, and ionization sites for several of these molecules in order to develop an activity-structure relationship. If your software can help me, I will gladly cite it in publications and presentations. -------------- Update as of September 25th: Marvin software has been indispensible for 2 manuscripts in preparation. Chemaxon will be properly cited in both. Thank you

We focus, using in silico approaches, on early stage drug developments (from hit finding to hit-to-lead) and aim at: * the development of new methods/algorithms in the fields of structural bioinformatics and chemoinformatics. * the identification of small bio-active chemical compounds (hits, leads, chemical probes) able to interfere with desired biological activities or facilitating the understanding of new molecular mechanisms (chemogenomics or chemical biology projects). * the identification of new therapeutic targets through bioinformatics strategies.

Our aim is calculating chemical properties of small molecule for docking simulations.

properties and 3D presentation of organic molecules

QSAR studies and chemoinformatics research. Teaching a module of Chemoinformatics of a Computational Chemistry undergraduate course for students of Bach. Organic Chemistry.

general lipids research

homology modeling, molecular dynamics, docking (so it is necessary to know the protonation of our molecule, Marvinsketch gives us this information)

We synthesized several heterocycles compounds (benzodioxins, benzofurans, etc) and stuied their biological activity (enzyme inhibitors, receptors agonist and antagonist activities). For the interpretation of these results, we would like to use the calculation of several properties (logP, logD etc.) of our molecules.

It is intended to use the software to calculate the properties e.g., logP, molecular weight etc. of molecules which will be generated using my own computer code.

The software will be used for comparing the experimental products and predicted products. Outlining the mechanism of product formation. esigning of chemical route for the desired products.

Used to generate data files for synthetic chemistry reactions. Chemical library enumeration.

Software will be used to calculate chemical properties of GABA analogues and other molecules acting at GABA receptors eg benzodiazepines, flavonoids. In teaching the software will be used to demonstrate various chemical and physical properties of drugs.

Current primary application of interest is to use the MarvinSketch applet to allow students using an organic chemistry learning system to input curved-arrow mechanism diagrams. Refer to \"Synthesis Explorer\" section of website listed below. Publication describing this system, which includes ChemAxon acknowledgement, is expected within a few months. Second major usage involves the MarvinView (and JChem?) components to implement a Java Servlet to generate 2D molecule depictions from SMILES strings over the web to facilitate browsing through chemical databases.

The aims of our research are to learn more about memory formation process. We do this through drug design and organic synthesis. We love Marvin SKetch for this reason - it is easy to share files and paste them into powerpoint for presentations.

Aspects of my ACEorganic online homework seem to require acquisition of a license.

its for making the students more acquinted with the chemistry by the use of software

I will use this software through all the course i teach, general chemistry, quantitative analytical chemistry, and instrumental analysis. Chemistry is a very visual discipline and the more students look at structures of molecule to understand concepts the better in my opinion. I will also be using the software for my research group when they need to do group meetings, talk about their research at conferences and on their web page. Journal articles will be published on the incorporation of this software in a website on flow injection analysis (www.fia.unf.edu) in addition to our scientific publications on chemical warfare analysis.

I am a PH.D student at University in Tuebingen. My research topic is design, synthesis and development of novel p38 MAP kinase inhibitors (Pharmaceutical Chemistry). For this topic your tools may help me to develop new inhibitors. For example: I would like to calculate logP values and pks-values.

I would like to use Marvin sketch to be able to calculate logp, logd and pkas of hydroxypryidinones, which are the compunds that my fourth year research project is based on.

this software will worked and implementing for visualization and labours of learning in the computers rooms of Chemistry Departament

To train students in the use of chemical graphics software and low level computational analysis tools.

The primary focus of my research lab is the design and synthesis of unique molecular entities that can be used to more fully understand complex biological problems. We approach this goal from two distinct pathways: (1) synthesis and systematic modification of known drugs or biological probes; (2) synthesis of libraries related to lead compounds in order to develop SAR. I believe that the suite of products offered by ChemAxon will allow us to better organize and evaluate the data that we generate, and help to focus our efforts on asking the \'right\' chemical questions.

We are conducting molecular docking study, and need to use marvin to generate different tautomers.

med chem

I plan to use the software for teaching at ETH Zurich in the course \"Introduction to Organic Environmental Chemistry\". The main focus will be on its use for chemical risk assessment.

I intend to use the MarvinSketch and MarvinView programs in handling small-scale QSAR datasets of novel in-house synthetised compounds with potential antitumor and antibacterial activity.

Chemoinformatics methodology: pharmacophore fingerprints, similaity search using fuzzy logics, QSAR

Chemical biology, HTS, compound library queries and analysis.

teaching pharmaceutical chemistry and computational chemistry - use this software for pKa and LogP predictions during laboratory exercises and for teaching the basics of molecular design

Teaching: mentoring graduate students and postdocs in modern drug discovery techniques; introduction of virtual techniques in drug design (med chem course, currently in development) Research: virtual library generation, filtering on properties, prioritization of compounds for med chem synthesis (properties, also with third-party software, like OpenEye).

anti hcv drugs

Teaching bioinformatics courses such as Structural Biology and Computer aided drug design. Designing drugs for viral targets and cancer targets like protein kinases and drugs for diabetes treatment.

The software will be used for teaching molecular modeling, QSAR and chemoinformatics.

Will be used for chemical structure drawing for publications and presentations and for estimation of compound physico-chemical properties (especially pKa and log P) relevant to environmental chemistry.

Advanced Science students will use tool to create and understand molecular structure for chemistry, biology, and environmental science. We are currently restructuring our department\'s curriculum to foster higher academic achievement for our more advanced students.

3D molecular database generation, for further investigations.

Simple structure drawing and manipulation.

- Teaching Chemistry 160, Graduate Quantum Mechanics - Research in computational chemistry

I\'m using dendrimers in organic photovoltaics, and characterizing dendrimers with XRD, absorption measurements, and AFM. I would like to use the geometry tools to approximate the size of the different molecules I\'m using and correlate that to distances found in XRD.

I am researching the gemetry og molecules

The basic solubility phenomena and some biological properties are due to intermolecular forces well reflected by five independent solvation parameters of solutes and five corresponding solvation parameters of solvents. The most accurate method to establish these parameters is very probably the gas-liquid chromatographic experimentation (GLC) with five different stationary phases. An alternative way is a simplified molecular topology (SMT), which principally takes into account, for each atom of a molecule, its nature, the nature of its bonds and in some cases the nature of its first neighbors. The SMT algorithm is based on the MarvinSketch program and other Java functionalities of ChemAxon Ltd. In a first step the molecules under study are drawn using the MarvinSketch program. In a second step, the Java library of ChemAxon allows to scroll through the molecular structures generated in the first step, in order to establish the needed parameters of solutes, i.e. of dispersion (δ), orientation (ω), polarizability-induction (ε), acidity (α) and basicity (β). This last step is achieved using suitable learning material from experimental origin.

I will use this software in the study of Stereochemistry ( Stereoisomers, conformations etc.) and for studying the geometry and properties of molecules.

70 PC stations with Marvin Molecules design by PH. D and researchers.

The software will be used to help develop separation methods for the analysis of developmental compounds used in the prevention of AIDS. The pKa, logP, and logD calculators will be particularly helpful in developing analytical methods to study degradation pathways of the pharmaceutical agent and its stability in formulation matrices.

I will use this program to predict pKa\'s to aid in purification of molecules made against T.brucei, the subject of my Thesis.

I plan to use MarvinSketch to render SMIRKS and SMILES strings into images for viewing and publication. Projects include exploration and machine learning on chemical reaction databases.

I need this software to assist me to do organic chemistry homework.

Our main interest lies in chemogenomics, by finding novel relationships between ligand and target spaces. Typical applications are the prediction of ligand selectivity for numerous targets or target selectivity for numerous chemotypes. As such, we develop and maintain several databases using ChemAxon products.

Will use Marvin for calculation of pKa values, needed for LC-MS/MS assay set-up.

Instruction in the use of NMR spectroscopy for structural analysis; preparation of research papers and reports on structural analysis by NMR.

I would like to use the software also for teaching and basic research purposes. Mainly for the conformational analysis of organic molecules and for the quick 3D visualization of the most stable conformers of the studied molecules at lab courses.

We are developing a web site to integrate malaria protein data with searches for possibly-associated chemical molecules. We would like to make some calculation functionality available for the selected small molecules in the system.

Protein ligand interactions

Course for Master of Pharmacy Undergraduates \"Computer technologies in Pharmacy\", \"Medicinal Chemistry\" Performing of in-house database searches, virtual screening.

I\'m trying to encourage students in introductory organic chemistry to become familiar with structure drawing programs as a both a pedagogical tool for teaching Lewis structures, and to help develop good chemical communication skills.

In silico screening of drugs. Pre-filtering of large libraries. Calculation of physicochemical properties. Browse and visualization.

I would like to use the software to calculate properties of our compound libraries for virtual screening.

The mission of the University of Kansas Center of Excellence in Chemical Methodologies & Library Development (KU CMLD) is to design and synthesize libraries that: * utilize new principles of scaffold design (and especially the incorporation of multiple scaffold cores into a single library) * are likely to have pharmacological activity based on sound drug design principles, and * are likely to have drug-like characteristics.

Termochemical conversion of solid fuels (pyrolysis). Analytical charactrisation of materials using Py-GC-MS/FID, IR, NIR, Termogravimetric Analysis.

Calculating chemical properties for QSAR

Currently I would like to use the Marvin tool for cleaning structures in Molfiles and converting them to InChI.

Coordination chemistry of tetraazamacrocycles with Gd, Tb and Eu

to show views of proteins for master students in biorganic and bioinorganic chemistry

Research on molecular imaging.

Research on molecular imaging.

Research on molecular imaging

Research on molecular imaging.

I teach General Chemistry courses and it is important having a tool for easy and fast molecular drawing. For my research, within my group it is always needed to draw molecules to have starting geometries for further work.

Basic scientific research about drug discovery for graduate study.

I do research on prediction of binding affinities of small molecules on protein receptors. I try to introduce different protonation states of ligand and see how the protonation states effect on binding. So I need a tool to calculate pka of ligand for it.

Radiopharmacy Coordination Chemistry

Capturing commercially available screening compounds and building blocks / intermediates Describing the synthetically accessible universe of compounds, reaction modeling and mining Statistical and non-statistical data analysis and clustering (in context of chemical information) HTS data analysis, structural features, pharmacophoric, spacial, visualization, protein receptor - ligand interactions virtual screening and QSAR

Teaching Chemistry to Year 11 and 12 (High school) students. Have found this tool very useful over the last 6 months, and using it has greatly helped the students understand their chemistry.

need to reformulate a databse of chemical reactions by balancing thier charge equation

Analysis of Chemical Libraries used for Screening

- I plan to build a small compound database for the computer literacy course. - I also plan to build a database of druggable compounds. This database will use to evaluate drug-likeness of each compounds.

Generating virtual chemical libraries and further screening of those molecules using Structure based and Pharmacophore based models

I am looking how to calculate pKa of stiryl dyes. Your program seems to provide a way to estimate pKa.

The software will be primarily used to gnerate 2D structures form smiles formats. This step is a part of developing QSPR models.

Presently we are implementing online chemistry courses for which we are developing structural templates for teaching purpose. Presently, these will be tested on our intranet network and later could be implemented on our webserver.

Searching for new metabotropic glutamate receptor mGluR2 and mGluR3 antagonists and agonists - database search, modelling, and syntheses.

chemical drawing and stereochemistry, application of chemoinformatics, searching in chemical databases, integration of chemical information into other programs

for the teaching of molecular modeling and computational chemistry at M.Sc. lavel and for our Ph.D. student.

I am interested in ligand docking to ligand-gated ion channels in nematode parasites. I would like to use your software to generate 3D conformers from SMILES strings.

Use for organic chemistry class

I want to calculate the pKa of proteins and atom charge of protein at different pH conditions by this software.

I am a biochemistry student who used your software and enjoyed the functionality and ease of use. I have recommended it to my friends who are involved in research, and would like to be able to use fully-functioning forms of the software for my lab courses and, in the future, research.

undergrad chem course

Protein structure prediction, Inhibitor designing and Molecular interaction studies

I teach courses in Organic Chemistry (1st-year) and other introductory chemistry courses. The software will primarily be used in the design of instructional materials, including PowerPoint presentations and on-line chemistry videos (like the ones I have posted on my \"old\" web site at http://faculty.riohondo.edu/mkoutroulis/chem230/video_main.htm I plan to develop a series of free videos for students on understanding organic reaction mechanisms.

To create problems and the answers for the problems for the students. Also to right lab reports and formal reports.

We aim to develop a library of small biomolecules for the treatment of metabolic diseasez.

Would like to test this software package as an alternative to Chemoffice for the preparation of images, primarily for assisting oral presentation of research results.

We will use the software for state-funded academic research. We also train students in the use of our software and its application in research. We do not have any Industrial cooperations which are profit-oriented.

modelling of ligands for protein docking experiments

I would like to see the conformation of 9-decyl radicals for illustration purposes in my research.

Investigating the geometric properties of ligands that are used for structure based virtual screening.

Would like to use in order to visualize compounds for my Organic Chemistry class.

I am a student in the organic chemistry series, Chem 201-203 and would use to help visualize what I can not fully grasp without seeing in visually in 3-dimensions.

The software provided by Your Institution is going be used to obtain the compoud\'s descriptors that can be used in the QSAR studies. Our actual projects concerns transition metal complexes with possible anticancer activity. Second area of our interest are the compounds with antioxidant activity.

To calculate pKa values and many other molecular descriptors for a collection of compounds. These descriptors will be used to analyze relationships between molecular structure and compound subcellular localization site.

My research interests are the cellular pharmacokinetics with drug molecules. So, I have to refer to the programs like chemaxon and marvin for the drug molecules. I plug in the parameters of molecules obtained from the programs into our model.

I wish to use the Marvin software to take a molecule and produce energy-minimized conformations in my research on potassium channel blockers. This research involves the computer simulation of how a ligand interacts with the channel.

Research on 5-ring structures in Organic Chemistry

Provide students with visual representations of molecular structures, particularly in their 3D conformations. Acid and base titrations will also be helpful in computer simulated visualizations. This in turn is helpful in understanding the concept of pKa, Henderson-Hasellbach theory, etc. The free resources offered by your company are advanced and comprehensive for such teaching purposes.

chemical graphical tool for Linux, quick determination of elemental analysis data, number of possible isomers

Graphical representations and several calculations (especially pka values)

to create new thing which is useful& safe for human being.

My research group is currently conducting research on dye sensitized solar cells. We would like to develop a database of potential molecules to create these types of solar cells. We will include the structures, HOMO-LUMO calculations, uv spectra, etc. We would like to use the Chemaxon for front and back end database development. We are novice’s to database development and implementation and after extensive research into database programs Chemaxon appears to be the best program for to use.

To prepare the input files for molecular dynamic simulation; view and analyze the output of the simulations, etc.

phD student - chemistry - catalysis

managing database, converting file formats, clustering

software helping the demonstration of 3D structures

Model presentation of possibilities of modern computer pharmaceutics and analytical and physical chemistries. In collaboration with the department of medical and pharmaceutical informatics, ZSMU

evaluation basic compound characteristics during Ph.D. work

leanring organic chemistry

I wish to use this package to prepare lecture materials, powerpoint illustrations, and for students in my lab to make reports on lab computers.

We are working with some computational methods (mainly inductive logic programming) to predict toxicity in chemical fragments (drug design). We are trying to construct rules between toxicity and some molecular descriptors. So we would like to use GenerateMD (mainly) to generate these molecular descriptors. Thank you.

Hi, I\'m a Pharmacy undergraduate. I wish to apply for the license to use the various calculator tools as i find them invaluable in helping me to understand the various physicochemical properties of the drug molecules.

use for research purposes at the University of Cambridge in the field of dynamic combinatorial libraries. The software will be used for estimation of pKa and LogP

Registering and Analysis of structure/activity relationships of biologically active chemical analogs.

I use MarvinSketch to draw molecule to perform docking studies with AutoDock. I\'m interest on anti-HCV compounds.

I am teaching medicinal chemistry and drug design. in these courses we interesterd to learn the students: how to generate 3D shape of molecules, how to generate conforms, to visualize 3D shape of proteins....etc

Master Degree in design of bioactive molecules with potential therapeutic interest. Current research on design of libraries of modulators of sphingolipid metabolism.

I\'m doing my PhD on Drug discover, the work i\'m carrying on is based on synthetize new TRPV1 inhibitors. For that porpouse I have to calculate some LogP in order to find some clues about the sorroundings of the binding sites. ChemAxon will be used for the prediction of molecular descriptors, and estimations.

QSAR, computational chemistry courses, drug design

My Ms. Thesis is on the field of Drug Design with small molecules.

The design of fluorescence organic dyes

I\'ve used Marvin software for drawing moldecule. Nowadays, I\'m studying HOMO/LUMO level calculation of inorganic molecules. Marvin softwares give me a wonderful view of molecules!!! I really want to use Marvin software to keep studying more easily. Thanks a lot.

I will be using this with my AP Biology students to learn organic and biochemistry in a more visual way.

I want to use this software to show students about the 2D and 3D chemical structure ,show them the meaning of the logP,logD,pKa and other Phisycal Chemistry Knowledge.

I am working in field of computational chemistry mainly ab initio computations. Now I need to work with large database of molecules, compute several physicochemical property predictors and use this in statistical analysis. I am only a beginner in this field but several colleagues recommends me Your software.

I am a student.

I\'m going to use your reactor to create database for VS and for driving my medicinal chemistry research in the field of Ovarian Carcinoma therapy.

I need this program to find out the real structures of some molecules and syntesis of some organic chemicals.

Chemoinformatics related PhD; Marvin used for visualisations and caluclation of molecular properties. JChem in combination with Instant JChem to manage libraries of molecules in a standardised way (Standardizer), overlap analyses with Instant JChem.

I am Professor of Chemical Engineering and Biotechnology and am in charge of teaching some Pharmacology, Drug design and discovery.

Synthesis

Database application for metabolomics research

To be used in graduate work for the estimating/predicting of physico-chemical properties of environmetally relevant compounds.

investigations related to dynamics of molecules in solution

To investigate aspects of ADME properties, decomposition and fragmentation in relation to drug metabolism. To teach phD students relationship between compound structure, physchem parameters and ADME behaviour.

Topological structure analysis for gas phase electron diffraction evaluation and structural refinement.

I use Chemaxon\'s Reactor software to generate virtual library of compounds for docking studies.

I teach chemical kinetics to 4th year chemical engineering students, and am considering introducing Marvin to in my class. My aim is to make chemical engineering students aware of computational tools used by chemists, and apply these tools to assist in model the performance of chemical reactors.

computational chemistry

Test the program package for research (QSAR) and teaching (medicinal chemistry) purposes.

pKa and pI prediction from structure of small molecules

I need to generate pharmacophore fingerprints and fuzzy pharmacophore fingerprints to analyse the impact of different metrics on it. I\'have already use generatemd and present a poster in Budapest.

Use tools from ChemAxon to clean up the molecular structure. And implement novel machine learning method such as Distance Weighted Discrimination (DWD), to perform a QSAR study on a set of compounds from NCI.

I am using this for organic chemistry help.

I would like to use these tools to help with organic chemistry.

Hy, I want to mapp reactions in order to run my programms to try clustering algorythm. Thanks, Aurélie de LUCA

The purpose of our research is analyzing diversity, topology and few other computable descriptors of structures from the GDB, WOMBAT, PubChem etc. databases. We suppose that inst.jchem with mysql will be the best sollution for this task, as far as we need to run advanced sql queries.

studies on hybrid materials

Prediction of logP, pKa and metabolism of drugs under development

Benefit of our members\' multiple disciplinary background, our research interests are pretty broad. However, our research objective is predifined to use Bioinformatics knowledge and technologies to facilitate the understanding of biological/ medical system and rational drug design. Currently, our research interests can be specified in following directions: Druggable Genomics/Proteomics; Development and application of biological databases and software; Bioinformatics-aided Drug Design; Data mining; Evolution;

We aim to calculate additional properties for a set of compounds which used as inhibitors of CAR-enzyme. Study is fully academic and we need to make principal component analysis to cluster the compounds.

Modulators of biomolecular interactions. JChem will be used for research and occasionally to train students in practical courses on NMR spectroscopy. Online implementation is not planned sofar.

enzyme engineering

Forensic analysis of archtectural paints using Raman spectroscopy Raman spectroscopy applied to the forensic analysis of trace evidence The chemistry and molecular interactions of pigments in paint

computational drug design

We study the mechanism of action of different drugs (our main interests are sodium channel inhibitors and drugs acting on the CNS). We study theoretical aspects of receptor and ion channel kinetics, pharmacodynamics and related questions of drug distribution, effective concentrations, microspecies distribution, etc. For the study of action mechanisms, we use automated and manual electrophysiology techniques . The main idea is that different mechanisms of action are probably due to different binding sites, thus different biophysical properties of inhibition can be correlated with different chemical properties. Defining the set of chemical properties that allow effectiveness by an individual mechanism (i.e., at a certain binding site) would allow more intelligent drug design for that site. We plan to use Chemaxon softwares for building a small database of drugs, to compare their structures, and to calculate certain chemical properties.

pKa calculation for various compounds

Marvin required to use ibabel with openbabel under OS X. I am currently undertaking DFT studies of nanoscale structures, such as simplified SPM tips, and adsorption and self-assembly of organic molecules on metallic surfaces.

To calculate Log P of compounds used in cancer research.

Chemo-enzymatic synthesis of (S)-citalopram and Its Molecular Simulation and process Kinetics Study Lipase catalyzed remote resolution of citalopram Intermediate was studied.The binding mode of lipase and citalopram intermediate should be proposed by using molecular docking and molecular dynamics simulation methods. To develop the separation method of citalopram diol intermediate from its acetate using solvent extraction,the dissociation constant and distribution coefficient of citalopram should be caculated by molecular simulation.

charge distribution and dynamic of molecules

Prediction of physicochemical properties of some corticosteroids

I\'m a master student in Advanced Chemistry, photochemistry and photophysics.

Diversity of secondary metabolites

This sofware will be used for molecular modeling and drug research.

I would like to test the ability of Marvin to generate conformers of small molecules.

modelling the nano-scale systems e. g. nanotubes, protein modelling, phase equilibrium simulations

Organic chemistry

I am lecturing amongst others the general chemistry course and am responsible for the organic chemistry lab courses during the first two years of study. I would like to use the package to render 3D molecules look at pKa values, plot electron densities and so on. I am using linux and your software is the ONLY package that I know of that offers all thiese functionalities.

I\'m working on prediction of ADME properties for applications in virtual screening

This software is used for a current approach for transforming compound dataset into fingerprints. The output fingerprints will be used as input for a clustering algorithm.

evaluation and then use for teaching. will get back after implementation

This software will be used to draw molecular structures to include in scientific papers.

Plan to use when helping with organic chemistry tutoring.

for generating IUPAC name

I am not sure exactly what you mean by implementation of the software. I intend to use it mainly for drawing chemical structures and maintaining a database of out chemicals in the lab.

Strucuture properties relationship of peptides. Drawing peptides and organic structures, calculating properties such as pKa, pI, logP, charge, mass,..

Main usage will be the maximum common substructure calculation for molecule similarity.

I have a brief interesting in crystallographic region. The relation ship of structure and its properties is not so cleared that we will make a proto type of database.

We are currently working on large-scale docking studies of molecular libraries to identify interesting compounds that bind to various receptors. We will be using the software for analyzing and organizing our results.

Machine Learning for Predicting Phospholipidosis

Visualization of chemical structures.

Further development of the online organic chemistry homework program, ACE Organic, and use of the new functionality for teaching students at the University of Kentucky.

Bioaccumulation

Proposed usage to calculate pKa values, to demonstrate different ionic species in aqueous solutions and also non-aqueous media.

I plan to use the software to determine the protonation states of organic molecules. Correct protonation state may be necessary in molecular modelling / docking, which is what I plan to do.

An applied chemistry study unit is being developed to show students applications of physical chemistry in dosage form development. Predictions of various physicochemical parameters will be needed to assist in analytical method development, solubility predictions, and stability determinations.

Organic chemistry study

* Teaching molecular modeling in Biophysical Chem and Reaction mechanisms courses. * Calculating some physico-chemical parameters for QSAR applocations.

Use to find pKa

I currently teach courses at the undergraduate and graduate levels and would like to incorporate basic informatics tools, and for this purpose I would like to evaluate chemaxon. I may use it for research as well and can provide citation info in that eventuality.

chemoinfomatics and drug design

To use product to aid medicinal chemistry teaching in our pharmacy program

To help for projects in the determination of LogP. Used also for database registration (SD files)

creation of a chemical database for self-sythesied compunds

Property and reactivity estimation for environmental chemicals.

study of molecular dinamics

i\'m a student and i want use this software for learn more

Used as part of a drug design and development module given to undergraduate pharmacy students in their 3rd and 4th years in order to give them an appreciation of how in silico techniques can aid the drug discovery and development process.

To find out the structure details and physicochemical characteristics of proteins.

Research: Chemistry of Natural Products, mainly from plant species found at Brazilian savannah Teach: to be used by pharmacy undergratuated (to learn about how draw and calculate)

The students of my high school work fine with MarvinSketch. But they want to go further with the configuration for example.

I am supervising a number of graduate students doing research in synthetic pharm. organic chemistry

Comparison of databases

Optimization of pharmaceutical dosage form. Active ingredients and esxcipients characteristcs via molecular modeling. Data-mining procedures with use of artificial neural networks.

Interested in you excelent log D calculations for drug-like molecules.

Please, I would like to request an academic license for the latest versions of J_Chem; marvinbeans windows; and instantjchem for windows. It is used for teachinga nd research Thank you in advance

My main area of research is the discovery and application of multicomponent reactions. I will use Chemaxons software mainly for the generation of virtual combinatorial libraries and the calculation of the physicochemical properties of the members of those libraries.

I believe very strongly in the extensive use of visual supports. Right now, I do not have any molecular modeling software, so I am unable to create my own images. I will use this software to create models for PowerPoints, illustrations, handouts, and exams.

virtual screening for drug discovery

Handling libraries of small compounds used for screening against receptors.

The project is concerned with the design and application of methods for the thermodynamic and biosynthetic analysis of the metabolic chemistry in order to improve the understanding of the thermodynamic properties of metabolism, the thermodynamic limitations of metabolism, and the biosynthetic potential of metabolism. New pathways in metabolic networks will be simulated and analyzed. Moreover, the generation of new species and metabolites will be analyzed and classified. For this reason, software, such as Marvin Beans, and Jchem will be entirely useful and necessary in order to generate charged mol files and to classify and organize database information.

Work with the datasers for QSAR analysis.

We are interested in chemoinformatics and computer aided drug design. Recently our research need to enumerate the scarfold of databases. We use HierS program to perfom this task, which need jchem.jar to run. Also, I was looking for a chemoinformatics platform free for academic usage, used in our research and teching. Thank you!

We wish to include Marvin on our web-based submission form for x-ray structure analysis. We are currently holding a previous licence for this, and would like to update to the newer version

Structure determination of proteins in the presence of small molecule ligands

Molecular studies using molecular viewer as this, and i am interest in the tools of molecular representation that allow me to develop a theoretical studies of different molecules.

Molecular modeling studies for the design of new non-nucleoside reverse transcriptase inhibitors (NNRTIs) that are active against wild-type and mutant strains of HIV-1. Construction of 3D pharmacophores from structural data of macromolecule/ligand complexes. Virtual Screening.

Ligand designing for reserch in chemical biology. For example, DNA binding ligands, aptamers, affinity labeling reagents, etc...

Our aim is to give clear idea about chemistry tools and its application and how can we work the available tools .

For teaching experimental chemist how to use computational tools

teaching organic chemistry

I plan to use the program as an aid for my organic chemistry class.

Luminescence dye research

Drawing and calculating molecular properties

Red/Ox Enzymatic activity fundamental studies and protein immobilization on nanostructured surfaces to new generation biochip development.

My previous license no longer works with the new version of Chemaxon software. I get this error message when I try to import the old license: [Fatal Error] :1:1: Content is not allowed in prolog. org.xml.sax.SAXParseException: Content is not allowed in prolog. at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:243) at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:287) at (…) Could you please help me or send me a new license file. Thanks Marco Neves

I want to use JChem as a tool for molecular modelling and visualizing. I am utilizing it to calculate LogP or other molecular properties. I am still evaluationg JChem and I don\’t know it at all.

Calculation of logP values with undergraduate and postgraduate Pharmacy students.

I would like to try using this software for development of electrophoretic methods and pKa calculations. After discovering all the other possibilities probably I will use it for all other things as well.

The study of antimutagenici compounds in salted vegetables

Molecular Modelling of Proteins Molecular Modelling of Carbohydrates Experimental Oncology

The project aims to use computational drug discovery techniques to discover small molecules that may prevent the elevation in serum Retinol Binding Protein (RBP) and its effects and thereby prevent the development of insulin resistance and type 2 diabetes and to sustain and enhance an already funded experimental project to this end.

Polymorphim of medicines.

calcul logP

I use an electronic lab notebook system and require a user friendly drawing package to quickly input reaction diagrams – other features of the program will be evaluated as I use them.

To teach applied chemistry to undergraduate student of pharmaceutical sciences

Preparing lessons handouts and web applications

Reserch for Carbon Nanotube-DNA Hyblid.

Computational Minicourse (for organic chemists) Analysis of CMLD library (an NIH sponsored Center)

Tools provided by this software are very useful, especially under linux operating system in order to explain students how to calculate and use Physicochemical Properties of their molecules.

Visualisation of new molecules

Beta lactams drawing 2d to 3d convertion for publications

not really using for teaching, but to be able to calculate logP and logD in the lab. IT department has wiped out my laptop and I lost all my chem and bio programs including ChemAxon\’s software. Now I do not know how to re-acquire the necessary activation software

Will primarily used for its structure and reaction editing functionalities and may be referenced for theoretical calculations (LogP, LogD, etc…).

I would like to use this application for different purposes: 1. set up a database for storing syntesis product along with biological activity to easily obtain the information. 2. Database for the commercial starting materials we own and so to facilitate the structural search for realizing our synthesis program in medicinal chemistry 3. evaluate the possibilty of the program as tool in the medecinal chemistry (log P calculation, …) 4. Develop web-based application for students to allow them to visualize 3D structure.

I\’d like to build a database for NMR spectra that PhD-students gather during their promotion time. But honestly I\’m not sure if my knowledge of mysql/php is good enough. I\’ve created already database for their x-ray structures, but there is no possibility to search (sub)structures but only summary formula, student name, and crystal cell. These are quite satisfying as amount of x-ray secured structures is very limited (~10 per student). If this database reach beta-status, it will be hosted on computer which is available only from our institute 132.187.71.5 (all IPs are non-existing for outer-world — that\’s the policy of our IT-team). Btw could you send me a quote for academic price? I\’d like just to know the order of magnitude

I teach organic chemistry I and II, lectures and laboratories depending upon the assignment for particular semesters. Also, I am involved in biological chemistry research involving undergraduate and graduate students.

Use of JChem package for teaching of my ChemInformatics lectures. Research – improving high throughput docking procedures by various machine learning approaches trained on selected subset of 2D/3D descriptors.

surface analysis of polyester

For Class room Teaching and Laboratory Teaching in the field of Organic Chemistry and Hydrocarbon Fuels combustion

Teaching chemoinformatics

I used to use Hyperchem in my research & teaching post gradute students. I am looking forward to permit me to have the software for improving my carrier.

chemical drawing and 3D optimization

ADMET

The main objective of teaching is to develop thinking power of students.To achieve this & to make teaching effective,teacher uses different methods of teaching. The good method of teaching is seminar & projects &for this softwares like chemaxon help the teacher to far extent. Many difficult subjects can be made easy with the use of such a software. This enhances students basic understanding of the subject & also develops students interest in particular subject. This way teachers can make the classroom teaching interesting & meaningful. In particular,organic chemistry includes mechanisms,name reactions,spectroscopy,stereochemistry,acidity-basicity,aromaticity,molecular dynamics,historical background, 3D geometry,bond making & breaking processes,functional group conversion. Now we think that,if we use this software it will be more effective for our students from undergraduate to postgraduate for their syllabus & project work.

I am Vijayakumar S pursuing postdoctoral research with Dr. Michael in the field of protein modelling such as enzyme reaction, inhibition mechanism and also drug design. I am in need of the chemaxon softwar to do conformational analysis for acadamic purpose only. Vijay

Aim to build small molecule databases for virtual screening purposes. Need pertinent information provided by Chemaxon software.

I hope to use this Software for teaching undergraduate Pharmacy students aspects of pKa and lipophilicity, and also to use the software in research applications, e.g. SAR studies.

Usage for preparing chemicals for quantum chemical computations.

Biotechnology, Microbiology

Given a mol file for a metabolite at pH 7, we wish to convert these into a mol file at pH 7.7

I am currently doing QSAR studies of Cannabinoid 2 ligands and would like to use the Charge Plugin to calculate the partial charges of atoms to be used as a possible descriptor.

I intend on having my students use Marvin to calculate the energy of conformations in our organic chemistry lab and to use these calculations to predict the outcome of a reaction.

I\’m working in drug discovery through in silico screening. I\’m interested in this product because it seems to be a great package which can help to solve the every day issue in my work.

My study is to predict drug transfer into human milk. It is said that low molecular weight, low protein binding, and highly lipophilic drugs tend to transfer into human milk. So, I want to know logP and logD values for drugs as barometer of lipophilicity. But in many cases logD values at plasma pH don\’t measured. So I decided to obtain logD values from prediction software.

Comparing with ISIS Draw Drawing&Analysing smole molecules Do some QSAR research

I am currently developing an online course and I would like to draw chemical structures for this course. I would also like the ability for the students to be able to scroll over the structure of the compound and for pop-up text to appear explaining important aspects of the compound. I will not be making any implementations to the software.

I teach chemical information at Beijing Union University, and I will use some softwares of ChemAxon in my teaching job.

I will use it as a tool during my 6 month internship. I want to evaluate this program and see if it meets my needs.

I want to use software for rational drug design

My current project, electrocatalytic oil hydrogenation, is an alternative process, in which protons and electrons are generated on the catalyst surface at the anode and then transported protons react with unsaturated fatty acids at the cathode. The objective of this work is to develop a suitable catalyst to provide better selectivity and lower TFA content for the oil hydrogenation process. To fully exploit the promise of this novel process, it is also important to clarify the electrochemical hydrogenation and isomerization mechanisms. We propose to explore the use of early transition metal carbide based catalysts for the electrochemical hydrogenation of vegetable oils because these materials have been demonstrated catalytic properties that resemble those of platinum group metals. My current work includes synthesizing carbide and nitride catalysts, characterizing these materials, preparing membrane electrode assemblies (MEAs), operating the hydrogenation reactor, and analyzing oil products to evaluate the performance of these catalysts.

Development of a model for logP. I want to use the pKa calculator plugin to check that the values used from literature are in fact logP and not logD.

My search is arround virtual screening of the enzime inhibitors, molecular modeling and other areas of the drug desing

Our chemist asked to evaluate how / if we can integrate your software in our normal workflow.

Demonstration of protein and nucleic acid dynamics. Evalulation/calculation/display of electrostatic potentials

Development of an application for the storage and the management of a chimiothèque in the laboratory. It is not an activity of research but a service with the researchers.

Development of new gadolinium contrast agent for MRI, conformationnal calculation, NMR coupling and spin-orbit properties calculations.

The differences in the structure and function relationship of myoglobin in diving and non-diving mammals. I aim to identify differences in pKa and isoelectric points of Mb between divers and non-divers and differnces within the amino acids themsleves.

Drawing structures for display in class.

Molecular Structure and 3D Modeling Materials Science Molecular Dynamics and Conformers

We are a synthetic organic lab with a medicinal chemistry research agenda. We are currently investigating semi synthetic antimalarial drugs as well as analogs of Vitamin D to be used as a cancer chemotherapy.

This software will be used as a supplement to the lab courses.

teaching an elective in biodiversity and bioprospecting for PG students of science with some emphasis on chemoinformatics, molecular visualization etc. as also a full paper in future in bioand chemoinformatics Drawing known molecular structures, getting structures from IUPAC names, understanding properties of structures, viewing in three dimensions Tutorials would be given to the students in the class to learn and practice

Drug design, docking, screening

Design of inhibitors of Microtubule dynamic instability.

Calculation of logP and other various chemical properties.

IN AU-KBC RESEARCH CENTRE WE ARE TRYING TO UTILIZE ALL THE APPLICATIONS OF YOUR TOOLS

I wish to make use of your MarvinSketch package and associated plugins for the editing and presentation of compounds in my upcoming lab reports and academic projects as part of my masters degree.

Teaching Chemistry in Sixth Form

My aim is to teach the very basics of organic chemistry (school and high school level) with the model kit and web animations. Method is: Students choose molecule (say butane) from the list and get to the preparing page to reserve the parts that are needed to build the model. After that they launch the gif animation and build the model. At last (and this is where applets would be handy) they check their model rotating the virtual model. Till now I have used Chem3d-plugin on the checking page but Marvin applets would suit much better here. As You can see, the needs of my educational package would be rather moderate, simple molecules and only rotations by the user (MarvinView?). The site is public, non-profit but only in Finnish. I have also made another site for many years ago (http://pelu.jns.fi/~iroi/mol/) using Cherwell\’s appletts, but it has almost come to it\’s end. Name: Ilkka Roininen email: ilkka.roininen@kolumbus.fi

I\’m teaching Organic Chemistry and for activities and worksheets I need a program like this.

Organic Chemistry, NMR Spectroscopy, MS Spectrometry, Heterocyclic chemistry

Estimation of pKa values and solubility in order to optimally plan following experiments for experimental determination of those parameters.

Drug discovery

I teach biochemistry and molecular visualization courses at RIT. I am also involved in the Structural Biology Extensible Visualization Scripting Language project (look for SBEVSL on Sourceforge.net).

I include structures in the biophysical chemistry classes that I teach. In my research, I will be screening small molecule compound libraries for activators of PKR, the RNA activated protein kinase.

to investigate physical properties of some compounds

Visualization of molecular model on Mac, which used to be done by Chem3D.

Identification, creation and understanding the pharmacophore and applied this method to identified new potential compounds.

Ligand/library preparation process in virtual screening; lead optimization

For use in the interpretation of chemical names from patents.

Research: structure elucidation of organic compounds using different spectroscopic methods (MS. NMR, UV, IR) Teaching: mass spectrometry and bioanalytical chemistry

Research will include molecule drawing to aid in synthesis. We will employ as many features of the software as possible. Teaching will include mentoring students in synthetic methods and molecular design.

To identify various pKa values of various compounds.

Sophomore Organic Chemistry Lab students will be offered a download of MarvinSketch. The installation file download will be posted to the university\’s secure Blackboard course website, to which only the students, TA\’s and instructor will have access. Students will use the software to generate electronic illustrations for laboratory reports.

Courses on pesticide chemistry and environmental toxicology

I recently had to reformat my hard drive because of a computer virus and I therefore need to reinstall ChemAxon. I would like to continue to use it to predict pKa values and as a chemical structure editor. I have submitted a paper, which cites ChemAxon, but it is still under review. ————————————————————————— At this time, I would like to use Chemaxon to predict pKa values of compounds identified in a high throughput screen.

I am working as a Professor and Head, Department of Applied Chemistry and pursuing research in the field of Computational Chemistry with an emphasis on Molecular Modelling and Drug Design.

Chemoinformatic modeling of enzyme inhibition

Bioinformatics and molecular modeling

Predicting of physicochemical properties for mol. modeling purpose to rationalise the development of \’drug-like\’ design molecules

Drug design and molecular modelling

I am starting a new course at our institution for computational approaches to chemistry/biochemistry. What you offer appears appropriate for the class that I envision. We are aggressively expanding our Masters program in chemistry, and your software would be a great help in teaching our students about state of the art computational methods.

Immune modulation by di- and tri-peptides. Novel anti-inflammatory molecules. Pharmacophore identification.

Research compounds

references and development

synthesis of heterocyclic compounds , study of their physicochemical, and biological properties search for bioactive molecules against cancer, alzheimer\’s disease, bacteria

Organic Syntheses

General and Organic Chemistry

BioC 3021 is a one-semester general biochemistry course for life science majors who are not majoring in biochemistry.

We want to train our pupils in: - Use of friendly cross-platform software. - Representation of organic and peptidic compounds in 3D. - Construction of complex molecules and extraction of important features, such as charges or partitioning or surface area. All these capabilities are thought to be an important part for molecular design subjects in Biochemistry/Biotechnology careers. The web implementation is expected for easy access. It is also expected to use the software with research purpouses.

I\’m a student at the University of Groningen, and I do a few projects, for example OLED\’s.

Teaching introduction of organic chemistry

Conformationally restricted nucleoside analogues

My idea is developement of some tool based on your products which could serve for chemometricians which deal with QSAR modeling.

As a supplement to classroom lecture

This software will be used for calculation of logD values and other molecular modeling utilities for library generation and screening. Additionally, its utility for compound library managment, curation, etc will be evaluated.

I am a postbac chemistry student, doing my requirements to do a Master\’s in Biology later. I found the link online while looking for \”resonance structures\”.

My area of research: drug analysis and physico-chemical characterization of drug molecules.

This package will be used to help with my education in chemistry and biochemistry at Arizona State University.

Teaching students chemical informatics.

I am using this software to help in my organic chemistry class. I am a student.

I am working on molecular drug design. I need this package to calculate chemical properties of the hits that I found from our Virtual screening and docking experiments.

Used for making a workflow for drug discovery process. A virtual screening of Chemical libraries will be carried out by integrating jchem with oracle and other software. jchem is required for drawing and visualization of the molecules.

I am interested in virtual screening of chemical library. I wish to use your provided software to search through libraries. The overall aim for my research is to find selective inhibitor of kinase.

Draw chemical structures and reaction pathways for lectures and exams.

calculation pKa, logP, logD, charge, tautomerization, conformer and geometry

Software will be used strictly to teach and test theory on structures, properties, and reactions of compounds. Software will be used by only myself (instructor), with no electronic communication of any files that contain ChemAxon applications. As such, there will be no online implementation of any chemistry software.

I will use the software to draw structures for presentations and publications. I\’d also like to evaluate the other features

to calculate pKa values

Doing my PhD in chemistry

store biological activities of chemical compounds. evaluate chemical properties.

chemical structure database; qsar/qspr

Used to draw schemes and mechanisms for group meetings, presentations, posters and publication

Organic synthesis cource Piperazine chemistry

Use as database ant draw instrument

I\’d like to use ChemAxon products for drawing, prediction of organic compounds physicochemical properties and 3D structures representatoin as well.

Chemical structures frequently needed to be drawn to illustrate reactions and other ideas to students. Also useful for visualizing compounds.

primary structure of dna

I will use Chemaxon for structure visualization and management, virtual synthesis at a class (Multi Component reactions).

quantum chemistry, mechanisms of organic reactions, rearangements of long-lived carbocations

We intend to use Chemaxon tools to help in protein virtual screenning and to help in protein annotation.

We have just completed a high throughput screen and are interested in exploring the structural relationships between some of the compounds that tested positive in our screen.

Visualization of small molecules Documentation of molecular properties

research for a presentation coming up

I want to use Marvin for our drug discovery research

Students need to word process reports in organic chemistry. In one exercise, students are asked to redraw hand drawn chemical structures using a chemical drawing program and then asked to copy/paste their images into a MS Word document template. PC users in our lab are currently using ISIS-Draw and ChemSketch. Free chemical drawing programs for Macintosh users are not ready available. Mac users are using MarvinSketch with limited success because the \”save\” function is inactive without the license key.

Medicinal chemistry and drug design. Calculation of logP and logD of our products.

drug discovery by using combinatorial chemistry

The research in my group focuses on the development of new catalytic methods for organic synthesis. As such, we would use the ChemAxon software for presentations, our website, and possibly for publications.

As a research associate in organic chemistry, it is very essential to use chemdraw. For linux marvin is the best software according to the reviews. Hence i do want tio try it. So that I can use this one for my research as well as for teaching and for seminars.

Medicinal Chemistry: synthesis and drug design.

I am doing a PhD in material chemistry. I mainly use ab-initio packages to carry out my research work. I use MarvinSketch to produce nice graphics in my presentations, I am applying for a licence because I found that this software is able to compute useful properties such as molecular areas.

Use of relibase. Your program will be used for creating 2D chemical structures on a local basis.

Teaching organic chemistry (part of chemistry syllabus). Pupils/students 16-19 years old. Using Marvin to draw molecules for tests, presentation etc.

We want to find some isomers.

TACE a TNF-alpha converting enzyme a member of MMP family is new target for rheumatoid arthritis. present TACE inhibitors lack selectivity with other MMP`s. chemaxon will be used to find out structursl difference between TACE and other MMPs. there by drugs with selective action can be designed

I am doing QSAR modeling based on experimental data and try to improve the prediction accuracy of those modles.

I am looking to create QSAR models for toxicity. I want to make clustering with JKlustor… That\’s why I want to have the free lincense for my research.

Teaching undergraduate and graduate quantum chemistry courses. Working with students on quantum chemical calculations of metal catalysts and bioinorganic systems using, eg, Gaussian 03.

profiling of toxic compounds vs non toxic compounds

I am a graduate student at Emory University involved in astrochemical research. I have used MarvinBeans in the past for displaying molecules in figures and hope to continue doing so in the future. I also intend to make use of some of the more advanced features in MarvinSketch for interactive demonstrations in the undergraduate classes I must teach.

Quantitative relationships between structure and physicochemical properties of surfactant and modelling of surfactant partition between organic solvent and water/

We will be teaching students how to prepare structural inputs for their GAMESS calculations, related to their computational chemistry projects and research.

The tutorial offers an introduction to creating chemistry databases for PC users. Learn how to design databases, organize, edit, and use data in ChemAxon JChem. Learn to use the program\’s auto-assistance features and how to create custom chemistry draws in ChemAxon Marvin.

We are working in the field of lipid chemistry. The software is used by us and our students for structure drawing, pKa and other chemical calculations.

A brief description of the research or teaching implementation aims.

My research is to investigate binding domains between G alpha 12 and downstream effector proteins. Utilizing mutations of G alpha 12 in 6 amino acid sequences along the length of the protein, binding domains are established by interaction with a specific downstream effector protein. Once these binding domains are established, the mutations will eventually be reduced to 1 or 2 amino acid lengths. Ultimately, these mutations will be tested in vivo.

Using to help with homework.

The center will comprise a wide range of expertise and skills within its six research departments, with activities in the areas of disease systems biology, proteomics, high throughput protein production, chemical biology, disease biology, and protein therapeutics. The center will also contribute to the progress of translational research within medicine and provide fundamental insights which can be used to promote drug discovery and development.

I am a PhD student in the department of Bioinformatics in the Fraunhfoer Institue for Algorithms and Scientific Computing SCAI. The SCAI Institute organizes practical courses for students together with Bonn-Aachen International Center for Information Technology B-IT, in the Life-Science-Informatics Program of the B-IT Institute. I will use these tools for demonstrations to the students.

Organic chem research, visualization in 3D from flat 2D drawing to make concept less abstract.

Evaluate for suitability of student use in preparing structures for lab reports and special projects.

clustering and docking, file manipulation

Visualisation for molecular structures, tutorials, prediction of molecular attributes

I have course „Searching for Scientific Information“. Some parts of this course is about Chemoinformatics, representation of Chemical information, searching for Chemical Information, Chemical Data Bases, and useful Software for Chemics and so on. New information for this course may be very helpful.

To learn the IUPAC names

ChemAxon Package will be used in teaching the course \”New Informational Technologies\” for organic chemistry students.

Teaching chemistry and biochemistry to undergraduates and graduates;

I would like to use this package to create electrostatic potential maps of organometallic compounds for a short research paper.

Practical course of Computer Aided Medicinal Chemistry. Tasks to be accomplished: – compound clustering, comparison of different algorithms; – virtual screening; – pharmacophore identification; – ADME profile creation.

We are very much interested in all aspects of drug discovery. I have already established two lectures about biological assay systems and data analysis in drug discovery. Actually, I am going to devise supporting excercises using PCs and your software. At our department we put much emphasis on practical work. This means that students are early involved in different aspects of screening and data analysis. In hand on courses we are going to use your software package to teach the extraction of primary hits, structural clustering of active compounds, substructure and similarity searches in order to include close homologues of interesting hits into the confirmatory secondary screen to mention a few details. For these pratices we have some example data from former medium screening campaigns. Of course we would also like to use your software in ongoing research projects. It is one of our most important fundamentals to transfer knowledge obtained from research straight into teaching.

The main use of the ChemAxon software suite will concern design and properties prediction of compounds intended to be used in biology, biochemistry and cell biology. Further aspect of use might include isomers and conformers determination and use for in silico studies such as docking.

Physical and chemical properties of nanomaterials

I would like to use the software to draw the chemical formular visualize and organize the compounds for my study.

Wish to use in a new course (ChBE 734) developed on chemical and biological informatics. Plan to use Marvin Sketch for structure drawing, generation of SMILES codes and other representational formats, and to do simple property calculations (e.g., logP).

I am developing profiling and quantification methods for glycosphingolipids. Therefore, I need database for figuring out the characteristics of each molecules.

Drug Design and Protein Modeling

Illustrate pkA variation for small molecules. Visualize molecules.

Chemoinformatics manipulations will be done using the marvin view as well as calculations using LogP in nodes provided by infocom of Japan, within KNIME.

I want to use it for description of molecular structure and how different physical and chemical properties depends of these structures.

I am looking for an applet which can handle Lewis structures so I can add questions to current web pages that aid teaching General Chemistry concepts. PLease see http://undergrad-ed.chemistry.ohio-state.edu/ under the \”Gneral Chemistry\” link. If successful we would then like to use the applet to generate a test bank for our undergraduate students. See also http://chemunder.chemistry.ohio-state.edu/under/chemed/qbank/quizmain.htm If possible under the license agreement we would also like to add questions using the applet to the test bank within our course management system (D2L).

This software will be used in teaching of postgraduates and in research on systems biology and metabolic engineering. Since we are working on bioenegry using cassava and cellulosic materials as our feedstocks, the software may be helpful on illustration of the main ideas or technological pipelines.

I teach an honors organic lab (CHEM 213H) and an advanced organic/inorganic synthesis lab (CHEM 431W) at Penn State. I would like to give my students access to some additional tools–our institutional license for CambridgeSoft\’s ChemDraw is stripped of nearly all useful functionality. If any of these students find the Academic Package useful, I may be able to get some parts of it integrated into the curriculum. Although that is my main purpose, it is likely that I would use some of the resources in my personal research. I\’m not extremely familiar with all of the programs in the suite, but I would like to explore how they could be useful to me. Our research focuses on natural product synthesis and the development of new synthetic methodology.

The software will be used to set up a database to provide access to all the University investigators to the structure generated by ou laboratory. Alternatively, the database will be used for teaching in the new graduate program in medicinal chemistry. We did not have yet our own website and it will be set up in the new months.

Previously i got the licence and have been using, but i lost the licence file and that system got formatted. pl send methe fresh licence. Just now i have downloaded the installer.

studying chemistry

Initially I\’m just interested in the Marvin sketcher to include on a substructure search web page. I\’m unfamiliar with other chemaxon products, but would certainly be interested in evaluating them.

I would like to use the software to discriminate between amino acids, L, D and unnatural ones.

Develop trace organic analytical methods for detecting and quantifying pharmaceutical contaminants in wastewater with HPLC-MS and GC-MS Investigate removal efficiency via biological treatment by conventional activated sludge and the emerging membrane bioreactor Implement and model the operating paramaters to increase the removal efficiency

Calculations of pKa in order to fill some properties needed of some compounds.

je souhaite aider les élèves pour ma leçon sur le modèle VSEPR

developement of QSAR models and of Complex Networ-QSAR approaches to study and design novel compounds with biological activity, in particular novel Tyrosine-kinases and Topoisomerase inhibitor

Protein structure functiona analysis Drug disciovery and development Protein-protein interaction analysis

I will use it in construction of my models

i will test this software. It is wonderful. Thanks

Teaching Organc Chemestry

Chemical modification of polymers

I work in ADME/Tox QSPR environment.

Drawing Chemical structures for research papers

compound libraries design

We use thiol chemistry to affix lipid bilayers to solid substrates. We will be using this software to create graphical views of these chemical tethers for use in presentations.

connectivity map, gene expression analysis

teaching organic chemistry

Hello! We are studying cancer-related receptor tyrosine kinase Regards, Maxim

Calculation of LogD and other physiochemical properties of small molecules.

Anticancer drug discovery

Our research falls within the scope of molecular modeling. We are involved in several research projects, that encompass: - validation of molecular targets - assignment of functions to proteins - lead compound discovery - homology modeling In these projects we use virtual screening techniques, QSAR, docking and bioinformatics. We do no have any contracts or collaborations with commercial companies.

I am using MarvinSketch to evaluate logP and logD data for the surfactants we have synthesized and are currently testing. The results will be published in my doctoral dissertation, possibly a paper later this year.

Demonstrations in class, preparing hand-outs, making exam papers, and maybe post on my chem.is.try forum when needed.

I would like to use your software as a pKa and logP prediction tool.

I am evaluating the software for student use. My students will be looking at organic molecules and I want to provide them some tools to check their work as well as drawing molecules.

I major in cadd and biomolecular simulation.

I usually attend meetings frequently with my supervisors and collaborators, national and international conferences and i need to present my results in those meetings, as recently i bought MAC to have a better control on presenting my data and results, so need a chemistry software that can go along with it, though other softwares like ChemDraw is available under institutional agreements but its only for windows, i downloaded Marvin beans for MAC and it has very interesting features, but to get full use of it i request for single user license, I will send you the publications and documents those will have structures drawn in your software as i will get them completed, more over i will acknowledge ChemAxon in my national and international presentations and posters.

I am teaching chemistry for students aged 17-19 in a norwegian school. I am interested in programs to help me visualize chemistry on the computer. I was testing the Flowreact system and MarvinSketch, and was asked for a license key. Hopefully this application will help me get one.

teach organic chemistry research in medicinal chemistry

Teaching for molecular docking

my research mainly focus on the interaction between protein and inorganic complexes that are desinged to serve as potential drugs for parkinson\’s disease. I wand to use your software to build those molecules, to calculate their basic physical properties, and (if possible) to simulate and modulate their interaction with proteins.

Structures presented in course taught in spring semester: Biopolymers

Use features of the software to study hERGCPDB toxicity and carcinogens.

Research is being done in my organic chemistry class in which a synthesis is performed and this information would be valuable in being able to do so.

1.Handling Post graduate organic chemistry lab 2.Operation and maintenance of Sophisticated instruments like NMR,IR,UV-visible spectrometers, GC, HPLC etc. 3. registered as PhD scholar in the department of chemistry ,IIT., Madras

I will use this program to visualize molecules, add hydrogens, calculate charge and other.

We aim to investigate the effect of lipids on apolipoprotein amyloid fibril formation. we already have a variety of lipids that affect fibril formation, however we do not have any information on the physical propoerties of the molecules (ie hydrophobicity, charge etc…). this is what the software will be used for.

Organis Chemistry

Reporting and tracking of high throughput screening results.

I willl use all the pipeline to prepare and analyse virtual high throughput screening.

Pharmacy students will use the software to evaluate the protonation of drugs at a certain pH. This wil have a huge impact on analysis (extraction, HPLC, TLC, etc), bioavalabilty, drug formulation, solubility in different solvents, etc. Your software is great in showing where (de-)protonation occurs in the molecule and the consequences for logP/D. Also the molecular dynamics tool will be used to show students the dynamics of drugs in solvents.

I want ot use pKa prediciton tool of your package for finding the possible protonation states of small molecules. This is one of the step towards drug design.

With the ChemAxon application package my students and I want to - create and draw three-dimensional structures of important molecules (including biologically relevant ones) – especially study conformers and molecular dynamics; - compare experimentally obtained titration curves with dominant protonation state of a molecule (major microspecies plugin); - create and verify the naming of organic compounds by IUPAC nomenclature; - calculate logD values to clarify the hydrophobicity on selected molecules. Main goal is to prepare the students of my chemistry elective course for the Maturität (higher education entrance qualification in Switzerland).

Draw chemical structures, calculate molecular weight, calculate mass spectra.

Modelling of organic molecules at GCSE and A level. Modelling od reactions at this level, too.

I\’m just making pretty pictures of molecules for presentations.

This program will mainly use for the chemistry teaching and research

My research project is related to the virtual screening of databases of small ligands against pharmacologically important protein receptors. The aim is to identify potential inhibitors of such proteins. The research involves: o Sketching, visualising and editing ligand molecules in several formats e.g *.mol2, *.pdb, *.sdf, etc. o Assign correct protonation forms to molecules. o Calculate a number of physicochemical properties e.g. logP, logD, pKa, HBD, HBA, Isoelectric point, PSA. o Comprehensive management of databases of ligands. ChemAxon\’s free Academic Package includes outstanding programs that cover many of the tasks in my research process. Therefore, ChemAxon suit of programs would extremely enhance my research. Thank very much in advance for considering my application. Sincerely, Sergio Mares-Samano PhD Student School of Pharmacy and Pharmaceutical Sciences The University of Manchester Manchester United Kingdom

My research is about the mechanisms of the regulation of the function of heme proteins. I use this program for research.

Similarity of molecules.

sorting and searching of databases of chemical compounds to determine structure/activity relationships for in vitro testing to prevent protein aggregation in various disease states in support of NIH grants. PhD students will be taught to use the software for handling data germane to their projects.

I intend to use the software and its results in lectures and laboratory activities within a course on separative methods in analytical chemistry. In particular I will use interactive lesson to let the students to calculate distribution constants and design experiments to verified their theoretical results. I have already used the on-line version of your software tools and I find it an extremely powerful tool not only to find out estimation of constants not easily recoverable in the technical literature, but also as a quick way to illustrate distribution of species and the effect of pH (for instance ) on partition. Also I use the sketch module to let the students build their molecule during their class or laboratory work

Study of Trees, and response to environment

I\’m making some research in so-called In Silico Prediction of Drug Properties. I need this tool to convert a list of Iupac Names to theis structural form.

Research

I plan to use Marvin to draw structures for PowerPoint-presentations used in seminars for students, Ph.D.-students and postdocs. Besides that, the software will be used to draw the structural formulas for educational posters featuring trivial names and later on name reactions. ChemAxon and Marvin will be mentioned for support on the posters and generated structures will be provided for import in the templates / name conversion tool as discussed with Alex Allardyce.

I have a current research license and would like to add teaching to this as well. I\’ve seperated the uses below to present salient details. Research: We plan to begin using Instant Jchem for our compound repository. We haven\’t used any chemaxon products for research to date but we\’re re-evaluating our software and may begin to do so. Teaching: We\’ve developed a drug discovery web portal for use as a research and teaching tool for academic organizations. This portal is hosted by the Ohio Supercomputer Center and turns any command line application into a graphical web service. The portal gather applications from distributed computers and offers then through a common website and manages them with a single user account. We manage both research and student licenses. For example, openeye requires each researcher to obtain an indiviual license which they forward to us to activate the ability to work with their own data. Student licenses simply enable students to work with data we provide in tutorials.

One purpose is the virtual screening research to find the drug to inhibit enzymes. Another purpose is teaching, if students want to study the above experiments.

propagation and popularization of chemistry, drawing chemical structures.

I submit chemistry assignments via Ace Organic and need the Stereoisomer Plugin to alter my answers.

The NIH Center of Biomedical Research Excellence (COBRE) for Structural and Functional Neuroscience at The University of Montana was established through the Institutional Development Award program of the National Center for Research Resources. The research mission of the Center is to utilize approaches at the interface of molecular pharmacology, synthetic chemistry, physiology, and molecular biology to advance our understanding of the central nervous system, particularly as related to protein structure and function, signaling, transport, and pathogenesis. The Center is also intended to serve as a core around which to develop infrastructure that benefits a much broader range of basic, clinical and translational biomedical research efforts in Montana. The Center is directed by Michael Kavanaugh, Ph.D., and Center investigators include faculty from departments including Biomedical and Pharmaceutical Sciences, Chemistry, Mathematics, and the Division of Biological Sciences at The University of Montana-Missoula. In addition to the Missoula campus, Center investigators are also located at the McLaughlin Research Institute in Great Falls and at Montana State University. CSFN is Supported by NIH Grant Number P20 RR015583 from the COBRE Program of the National Center for Research Resources.

predict logP

For Drug designing of Chk1 Kinase

Molecular modelling and visualisation. pKa calculations.

softwares will be in virtual screening and in QSAR.

I need JChem to help our lab build a natrue product database for virtual screening,aimed at finding anticancer drugs,and also do some QSAR jobs.

We are studying quantum molecular dynamics on several molecules, for which we need to design the optimized molecular geometry as input in the molecular dynamics code. We are using SIESTA and CPMD for quantum molecular dynamics.

Teaching senior Chemistry courses.

I am working in metal speciation in plant fluids such as xylem as phloem. I am also interested in the metabolomics of these fluids. I would use Marvin as a molecular viewer and also to make different types of calculations such as pKa etc.

cheminformatics based drug discovery and design

evaluation for research we plan to implement a fragment based lead discovery department in our university, and I am evaluating software (preferrably free) for molecular database handling, fragment docking and evaluation, and hit-to-lead transition.

Software wird genutzt zur Visualisierung und Berechnung der pka-Werte.

Yale is interested in evaluating your software for the purposes of teaching Organic Chem classes by our faculty as well research conducted in Chemistry, Physics and Engineering Departments. I represent Science & Research Software Core – the unit of provost office to support our faculty in scientific software.

Research in several areas of biochemistry.

The package will be used for learning how the partial and total charges as well as polarizability are formed in small molecules.

Calculation of pKa of 2D structures

I am working on the development of new protozoal drugs. Therefor I will use your software as a model/ tool to calculate more properties of my drugs and improve their activity.

I am studying crystallization, and will be using the pKa prediction to estimate where and if the molecules I am using will be protonated/deprotonated in solution, to help understand the phase diagram. The predicted pKa\’s may also help in understanding the binding in the solid state (hydrogen bonding etc). I may also use the 3d visualisation package to look at the structures of my materials in the solid state.

QSAR model for predicting toxicity

Using the software to teach many aspects of chemical properties

registering compounds in screening database

Development of SAR. Pharmacophore modelling. Predictive drug design. Lecture and class teaching preparation.

Molecular modeling for photochemical materials simulation – Validation of theoretical fenomenological model on matter transport in matrices containing photoisomerisable compounds. We need to simulate what is the most probable position of the average PMMA-DR1 chains in out system in order to make good hypothesis on a fenomenological structure for the photoinduced movement.

I am currently taking my second term of Organic Chemistry. Next semester I will have p chem and Biochem, and I am sure many more chemistry classes to come. I have been using the trial version and there\’s a lot of things I would like to experiment with but cannot do so without the Academic Package. I think this package would help expand on my knowledge and provide me with an additional learning resource and would really appreciate the opportunity.

Research use. For my study that I\’d like to use this software development new candiate compound from protein.

I will have my students use MarvinSketch to upload problems into my spreadsheet for comparison (SMILES). This will help teach them how to use molecular drawing software that can be used for creating lab reports. I am writing a grant (NSF CCLI) that will use MarvinSketch as a tool for a web-browser based assessment tool for the classroom. The purpose of the grant is to use open-ended questions instead of multiple-choice for STEM education. I had MarvinSketch working from my SFASU website, but now receive the following message: \”unsigned application requesting unrestricted access to system\” \”unsigned resource: Http://faculty.sfasu.edu/jefferya/marvin/lib/MarvinBeans.jar\” Will the new license fix this problem? Please advise. Thanks, Arlen Jeffery

Use chemaxon software to estimate some physical/chemical properties of some organic pollutants.

QSAR, HTS data analysis, clustering

To calculate descriptors for small datasets of natural compounds, fullerene derivatives, other organic compounds. Mostly I do structure-toxicity studies of different organic compounds.

evaluation for research we are looking for software for molecular database handling, in order to realize virtual screening using fragment based approach.

i am taking seminar on this software to teach our colleagues..

I am giving a synthetic tour for my natural medicinal properties class and need to draw some chemical structures

Chemaxon Reactor will be used to apply reactions to molecules identified as potentially active leads by \”in silico\” screening using a machine learning algorithm. The new compounds generated will also be screened to try and identify potential hits.

developing new Analogues of Linezolid

I\’m working in a software development team (called GIPSE) of the Life Science Department of the CEA (fundamental research in the biology area) and we develop softwares for researchers in biology. We develop an information system called PhenoScreen for the team of Lafanéchère Laurence, who is registered at Chemaxon. Phenoscreen uses, for the compounds representation, some chemaxon\’s products.

For teaching it will be partly used in practice classes. Also in supervision of master and PhD students. For research it will be used as supportive software for QSAR modeling.

_Calculation of pKa and others phisical and chemical proprierties of some potential ligands such as benzothiazoles, sulfonic and disulfonic aromatic compounds, azo dyes, etc. _Orientation of undergraduate and graduate students.

My scientific and research interests are mainly in the area of chemoinformatics and include the development of new methods and software.

Tool for undergrads to create identifiers for structuress that the have drawn

My research interests (http://georgiamelagraki.googlepages.com) include chemoinformatics, which aims among others to understand relationships between chemical structures and their functional properties. This requires the development of formal quantitative descriptors for chemical or macromolecular structures, and extensive use of statistical, data mining, and computational techniques with large chemical or biological databases. In this context, ChemAxon Software will be used for computer-assisted drug design. These methodologies employ principles of variable selection of descriptors most relevant to the biological action of drug molecules and afford predictive models of drug action that aid in the design of novel or improved pharmaceuticals. Ongoing studies include the development of new methods for data analysis, and the prediction and integration of these computational tools with experimental research. For teaching purposes I would like to include ChemAxon software in the Computational Chemistry Laboratory, in order to teach 2nd year students how to calculate basic molecular descriptors and design small molecules.

The ChemAxon software will be implemented in our laboratory for running our chemical inventory (chemicalinventory.org). No other implementations are intended at this point. If, however, they are used for other reasons in the lab or in my teaching, then I will update this information.

Demonstration of anaesthetic molecules

This software will be introduced in a practical course concerning the use of virtual tools for the organic chemist : I – Structure and reaction 2D drawing using JChem followed by creation of virtual notebook using Instant JChem. II – Introduction to structure database storage, management and search : Chemical Database elaboration with structural search using instant JChem or JChem for Excel. Chemical Library elaboration with structural search using instant JChem. III – Brief introduction to QSAR and 3D molecular representation (Smiles generation, pKa calculations, logP calculations, logD calculations, …) using Marvin Beans and JChem Base.

The application will be for fundamental research in life science and medical imaging area. My research are computational chemistry from quantum mechanics to classical molecular dynamics.

To develop pharmacological studies in the frame of clinical research.

perception of molecular graphs

Our Center focuses on the synthesis of complex molecule arrays. We will utilize the software for visualization and organization of these arrays.

teach student to design the new drug and the computer aided drug design

Use for molecular visualisation and database applications in academic drug discovery projects.

Hi! I would like to uso your program in my classes.

the polymeric gene vectors degardale materials for gene therapy i need to draw the molecule formula and the synthesis path using the softwares.what\’s more in my coming graduate education, the software needs such academic package

I am currently an undergraduate student at UC Davis majoring in Chemistry. I believe that the program will help me with my education in the Chemistry field.

To investigate to adsorption behavior of tolyltriazole onto copper under the influence of monochloramine

computational chemistry, chemoinformatics, structure-based virtual screening and design studies and courses

Microbial biodegradation of chemical compounds.

To draw biomolecues and calculate their properties for research purpose.

I am generating molecules in a consistent format to use in a review article

We are working on the inhibition of various nucleic acid polymerases including HIV, SARS and FMDV

In research we are interested in the design and synthesis of new biologically active organic compounds and in the fields of bioenergy. The software would be very useful in classroom for study of intermolecular interactions related to the structure of the molecules, among other topics.

Use chemical calculations for EPR spectra simulations.

drawing structures for presentations and postdocs

Clustering metabolite libraries for lead compound screening of protein interactions

try to dock substrates of BCRP (breast cancer resistance protein) and substrate of P450 to their targets. try to see the combine the chemAxon to make the small molecules for docking studies.

We are working on the development of a protein-ligand docking algorithm. For the setup of the ligand structures, it is important to get a finling on the possible protonation states, which can be formed in the active site of the protein. We are planing to use the MARVIN pka plugin to evaluate possible protonation states.

This software will be used to analyze the stability of aromatic compounds after the addition of various substituent groups on the aromatic ring.

drub screening (HIV-1 RT)

For teaching to M.Sc. Biotechnology/Biomedical/ Pharmaceutical Chemistry students – how to search Markush Structures, How to analyse the chemical and physical properties and other appplications etc.

drawn structures to improve QSAR-3D methods

Search for new antimicrobial and anti-trypanosoma lead compounds using in silico strategies

To demonstrate some principles of basic organic chemistry to undergraduate students.

The aim for Using this software for drawing 2D structure of chemical derivatives, measure bond angle and bond length. after the drawing the structure further use in Computer Aided Drug Designing and pharmacophore modeling. Other use in practical in teaching.

I\’ve been chemically modifying proteins to alter their immunogenicity, and wish to use the software to make drawings of the the reaction chemistry.

Knowledge about how enzymes function is fundamental to our understanding of life.

General Organic Chemistry and use in systematic identification of unknown compounds.

My first implementation aim is the visualization of molecular properties (charge, etc) in class (especially for the better understanding of complex chemistry and compound-solvent-interactions). Additionally I plan to test other functions for use in advanced courses with students.

Our aim is to explore correlation between therapeutic indication and chemical properties. While many drugs with different therapeutic indications inhibit sodium channels, their mechanism of action still unknown. We use automated patch-clamp to explore the mechanism of action of sodium-channel blockers, and JChem for characterize the chemical properties.

Analyse molecules (especially drugs)

fragmentation software package for similarities search

We are performing research in the area of materials for molecular electronics.

structure and ligand based drug design.

Organic chemistry for pharmacy students

LSIC\’s research topics concern modelizing chemical information and reasoning, and conceiving computer tools for managing and exploiting this information. At the same time, LSIC ensures some tasks within CNRS: * train academic chemists for a better use of existing computer tools for chemists (2002-2003 courses on Chemical databases) * promote the CNRS heritage (incentive to chemical databases development; project of national structure-based combinatorial library) * federate CNRS research teams dealing with chemical information.

Coordinated Practical Teaching

I am a student in The Institute of Chemical Technology in Prague and I am writing a Master thesis, the topic is comparison of IJC with other competitive software (Isentris, Chembridgesoft,…). For some tasks I need a license for Markush.

It will be used in the Medicinal Chemistry course for the computational lab modules and in organic chemistry to explore chemical reactions.

fast similarity search of chemical database

My PhD is within the field of Computational Toxicology. I intend to primarily use cxcalc for descriptor calculations.

I am a student taking the organic chemistry courses and I need a progam to sketch and react compounds, also to create resonance structures

Study and research of new drugs.

I\’m a student, i\’ve been desperately looking for a mac compatible chemical sketcher and to do some basic analysis. Would mainly be used for assignments and lab reports. Thanks

Chemical biology on chemotactic receptors of Peronosporomycetes zoospore

docking ligands with receptor histaminergic H3 Using all conformer of ligands.

We are planning to use some standardize in order to clean our chemical library and then to perform virtual screening over our targets. We focus our attention in GPCR research and also over HIV proteases.

We are involved in drug development, and so we are concerned by partitioning and pKa predictions.

biology and chemistry teacher, hischool

try to find more easy way to learn chemistry

I will be using this tool to assist me in organic synthesis to compute physical properties of substances and visualize the compounds.

Hi i am studying one of the cyanobacterial molecule as a drug. This molecule is a secondary metabolite. using this software package i can study its physiochemical properties, i can visualize its docked confirmations obtained from Gold and calculate the RMSD values.

Research on environmental persistence of chemicals including the degradation products or released or \”parent\” compounds. Software will be used for biodegradation pathways comparison and drawing structural analogies among industrial compounds.

Drug design and discovery through chemo-informatics approach

We are trying to use machine learning to better results of Virtual HTS screenings. We use molecular properties and docking results as primary data of our research.

physical chemistry , quantum chemistry

Instructional use in honors generalchemistry and honors chemistry laboratory

I plan to elucidate the correlation between physicochemical properties of drugs and absorption rate, especially in hydrophilic drugs. Generally I am using ChemBioDraw Ultra, ChemSite Pro, ChemSketch and PubChem Library. I need to calculate LogD, polar surface area and molecular surface area for hydrophilic drugs.

I am studying new angiogenesis molecules, in order to improve the inhibition effects that the hit molecule shows in vivo.

Structural biology : protein and nucleic acids structure Bioinformatics Crystallography

provide better understanding about drug-receptor interactons using chemical structures

my reserach interests are in polymer synthesis for biomaterilas applications. We intend to usethe software for predications associated with the responses of living systems to novel polymeric biomagterials.

My PhD student is titled: \”Computational Study on enzymatic process of interest in organic and biological chemistry\” I am a Teaching Senior Assistant.

To as a support tool for students research and analysis

Design and predict the Logp values of organic compounds with bioactivities for the synthetic methodology and drug discovery.

Removal of emerging contaminants from potable water.

I am designing novol antimicrobial agents to treat Pseudomonas aeruginosa biofilm related infections.

Our research group are interested in bioinformatic research. We are subscripted to the Havana university. Our investigations are close related with virtual screening, and informatics application of this area.

It will be used to draw molecular structure or to view 2D and/or 3D molecular configuration.

research

I intend on using the ability to calculate conformers and carry out molecular modeling to do a proof-of-concept check to see whether a reaction is likely to work. My area of research is in the development of new methods of enantioselective radical additions to alpha-beta unsaturated carbonyls. This involves the use of bulky chiral catalysts, as such steric constraints are the primary drivers of selectivity. I\’d like to know that my molecule is in the correct orientation in solution, and MarvinBeans seems like a cool way to do that.

I intend to use the software as part of my research project, which is in freshwater ecotoxicology. I believe the software will be valuable in exploring the chemical characteristics of the compounds whose impact in the environment I am interested in assessing.

biophysics

My research in the lab involves computer aided drug design. I plan to use ChemAxon for chemical structure visualization, evaluation and database management.

We are trying to evaluate compounds based on their physical chemical properties as it relates to their metabolism and bio availability.

I need it for the metabolomics research. Specially the small metabolite and hydrocarbons.

Exploring SAR in small series of synthetic molecules for undergraduate and postgraduate projects. Particularly interested in CLogP.

In our group, we are working in the field of Chemoinformatics and our aim is developing small molecules interacting with amyloid peptides in order to find new theragnosis agents for Alzheimer\’s disease. In the first step of this multidisciplinary work it is essential the use of JChem package for the in silico selection of best candidates from a large number of commercial compounds. Moreover, the subsequently application of structural filters as well as hydrofobic parameters (clogp, TPSA) and Lipinski\’s rules enables the selection of the best molecules for further chemical and biochemical assays. Recently, all these results have been published. Nowadays, we are working on the development of new molecules with different scaffold.

I am a grammar school student with medical ambitions and I wish to learn to use your software. I have seen it in use and I really like it.

The main use will be for performing searches of chemical compound repositories for structurally similar compounds. Additionally we would be interested in using the chemical sketcher for drawing the compounds to search for.

Currently working on my PhD in Environmental Toxicology. I will use this software for mainly structure images for my research

Physicochemical property calculation from compound databases.

Medicinal Chemistry teaching and research

I am a graduate student in the chemistry department at USC doing synthesis related to bisphosphonate drug discovery and triphosphate analogs. I will use the calculations available in the program to assist my synthetic endeavors.

The pathway of fragmentation of 2,4,5,6-tetrachloro-m-xylene

Visualisation and generation of ligand conformers in computational chemistry

Support of Scripps\’ NIH Molecular Screening Center (see http://mlpcn.florida.scripps.edu)

Iam doing 2D QSAR/QSPR research work. Iam mainly using topological index as descriptors. The Chemaxon plugin is excellent in calculating some rare descriptors like Sz index. This is the reason for my request. I will acknowledge Chemaxon in my publications.

I wish to use Reactor to investigate the applicability of established automated theorem prover software for new problem domains.

Preparation of structures for ab initio calculations

Teaching postgraduate students, usually on a one-to-one basis. Research in neuroscience, decision making for pharmacological tools, chemical properties.

structure based drug design

I\’ll be using these tools to investigate the different conformers and tautomers of fragments from different libraries, which I will then use in virtual High-Throughput Screening (vHTS) studies. These vHTS experiments will use AutoDock4.1 and different libraries of compounds to search for potential \”hits\” against multi-drug-resistant mutants of HIV protease (i.e., hits against the putative \”allosteric inhibitor site,\” which I discovered in my previous MD simulations……..which produced a cover article in Protein Science). These hits will then be modified, extended, and combined, in an attempt to develop new lead compounds (which could potentially be developed into new drugs). The ChemAxon tools will also be used to investigate the proper protonation states and conformational possibilities of the potential lead compounds that I design. I\’ll also use these ChemAxon tools to prepare compounds for docking studies against multi-drug-resistant mutant proteins from Plasmodium falciparum (i.e., the deadliest form of malaria). Since I\’ll be using ChemAxon tools to prepare large libraries of compounds, any advice that you can provide on the \”command line\” interface with these tools would be greatly appreciate.

Teaching: structure drawing, 2D & 3D representations. Research: using the tool for predicting pKa and compare results of calculation with experimental values.

Research work at the CEMES (Center for Material Elaboration and Structural Studies in Toulouse, France) on molecular-scale vehicles on carbon nanotubes with N. Picavet, supervised by X. Bouju & C. Joachim. Goal is to design a proof-of-concept nanoscopic-scale single-molecular vehicle moving along a carbon nanotube, with no other specific requirements. ChemAxon tools will be used to design and make various calculations on the proposed molecules.

For use in teaching chemistry to high school students.

To calculate molecular velocity in capillary electrophoresis

I will use it to learn organic chemistry.

3D visualization (not available in chemdraw for macs), general structure drawing.

It is research on adsorption of the substance to I want to calculate the ionization state in solution, pKa, and IP.

Currently i am working in drug development for Influenza A virus. i need to calculate the pKa value, logP,logD value of my newly designig durgs.

General design of biological molecules, analog searching and synthesis.

My research is involved with organic chemical structures. This program is useful for visualize new molecules

We would like to use your software to transform llinearly-written compound to its ring variants.

I will display some nice chemical drawing for General Chemistry Class.

I am evaluating the ChemAxon tools for potential use in a high school classroom setting. Project parameters include original ligand design and display of printed 2D and 3d structures.

Will use software to assess protonation state for in silico docking of compounds.

To give students a valid picture of how pKa varies with chemical environment

Software will be used to convert 2D compound databases to 3D compound databases so they can be used for docking and target site finding.

Creating structure files for Alexa 488/647 dyes used in MD simulations. Calculation of different conformations / creation of new .pdb/.mol2 files.

I want to use the program for showing true formular and structure of molecules to the students. Besides it is a good tool to name organic molecules.

Used in illustrating drug discovery concepts and molecular structure and dynamics.

I am beginning to use the internet to aid in communicating with my students. I want students to be able to include chemical structures in documents and web pages for assignments in my courses. To do this, I need an online chemical editor. I found Marvin via Google and am very impressed with it. The ability to estimate pKa values will enable me to add a new online exercise in my course where students can draw a molecule, estimate its pKa value(s) and then draw changes to its structure and see how the pKa estimates change. I look forward to exploring other features in Marvins and using them to enhance my student\’s experience in chemistry. The vast majority of my students are biology majors and a visual chemistry drawing program will give them an added ability to explore chemical structure with their eyes. Most are visual learners and this JAVA applet will be a great help to all my students.

Generation of starting structures and conformational search for modelling of reaction mechanisms. Visualization of results.

Instant JChem shall serve as a database server to store the structures (including identifiers and characteristics) of peptides and macromolecules which are derived from a combinatorial synthesis platform.

My PhD project will look at the action of sulphonylureas on white blood cells. I need to store in electronic form, drug structures and metabolites, but do not anticipate that the structures will be published after drawing.

I would like to evaluate the tools of chemaxon software and to compare its performance versus other similar packages.

I use this program for chemical representation in notes I give to fellow students and undergraduates. I also use this program to draw structures and perform work intended for use in a possible future publication.

I use the software to better understand reactions mechanism using the calculated pka values.

Development of UniPathway database: UniPathway is a metabolic pathway database used in UniProt knowledge base UniPathway web site http://www.grenoble.prabi.fr/obiwarehouse/unipathway UniProt web site http://www.uniprot.org

For better technique of teaching & for clear understanding of concepts of organic chemsitry. It well help aid in teaching organic chemistry to introductory college students.

to show the student how to see the structure in 3 D and its IUPAC nomenclature

I am trying to make a new protein in e. coli and I want to know its property.

As an useful tool to develop (specially in extraction/purification setps) analytical methods to determine contaminants in foodstuffs.

To evaluate properties of small molecule leads in high throughput screening

In our Institute we are doing research to discover new drugs against breast cancer. I received a license for the ChemAxon package (property predictions) but never downloaded because we obtained some commercial packages. At this point I would like to evaluate, and if useful apply, the new Metabolizer package in our academic drug discovery efforts.

Conformers, isomers of organic compounds

I\’m studying photo-induced phase transition.

For sketching and predicting physicolochemical properties useful in optimising ADMET for compound we synthesise

The main aim of my teaching and research is to teach and learn the different Chemoinformatics software to the students. Utilization of different software used in the Computer Aided Drug design and compare for the best is another objective of my research.

Teaching: advanced course of Drug Design, Research and Development in Medicinal Chemistry for pharmacy students; Bioinformatics and Biotechnology Methods for pharmacy students Research: 1) Search for new selective antagonists of ionotropic glutamate receptors (design, molecular modelling and docking, organic synthesis); 2) Serch for the competitive ligands for metabotropic glutamate receptors mGluRs 2/3; 3) New bacterial efflux pumps inhibitors among hydantoin derivatives

Hi Thanks for providing me the license for the instant JChem and marvin. I was wondering if i can use Jchem excel plugin with that license. Regards Raman

Chemcial Database Searching. SAR analysis. Chemical property analysis

We hope to use the software to investigate the chemistry of Corticosterone inhibitors in vivo.

project=Molecular grafting on oxide materials for energy storage applications Needs for molecule surface area and lenght calculations and for drawing

I would like to use the software for stereometric modeling in MarvinSketch through ACE Organic, to complete classroom assignments.

Proposed usage to visualize molecular conformations, studying tasks in 3D modeling of glycopeptides interactions and predicting of peptide-metal interactions.

Research: Our group\’s goal is to discover sterilizing antibacterials. 1. One approach is to identify prodrugs – compounds that have no activity on their own, but get converted into reactive compounds inside a bacterial cell by bacteria-specific enzymes. The aim is to discover prodrug antibiotics by screening compounds against strains overexpressing potential activating enzymes. 2. Another approach is to emulate the strategy used by medicinal plants to eliminate persisters. Plants such as Golden Seal make a membrane-acting antimicrobial berberine which is extruded from a pathogen by Multidrug Resistence (MDR) pumps. Plants also make MDR inhibitors, and berberine + MDR inhibitor produces a potent sterilizing combination. The aim is to identify MDR inhibitors that will be effective in humans and develop a combination therapeutic for sterilizing infections. Teaching: Software is used to teach graduate (mainly) and (sometimes) undergraduate students how to expand their HTS hits by building pharmacophores, select analogs, study in silico properties of molecules and assist them in the various aspects of their drug discovery projects.

doing protein engineering work, need to draw detailed structure of protein on chemical level

We would like to investigate the use of JChem for various projects in the lab connected with virtual screening, preparation of databases for virtual screening, clustering, similarity searching, and other related applications.

absorption mechnism research for TCM

To promote higher education of sciences for blind people or people with several visual disabilities, we intend to make accessible to them the perception of the molecular structures of organic compounds, as well the contents and concepts of Organic Chemistry, with support of Information and Communication Technologies (ICT).

Calculation of pKa for small peptides like Glutathion and amminoacids

Ligand Based Virtual Screening for hERG potassium channels activators

The aim is to import multiple molecules into Excel and analyze the properties of them after virtual screening.

The soft will be applied to confirm a compound I synthesized. I want to use it construct the model of the compound and calculate its low-energy structure.

This will be a perfect tool for a calculation of properties of numerous organic compounds that we use in our group. We mostly work on separation techniques – HPLC, EFLC, SFC, SEC, IEC, 2D-HPLC, TLC, extraction, CEC, MEKC. Selectivity and efficiency of separation process depends strongly on physical properties of compounds studied. Better knowledge of conformation, geometry, and possible interactions between molecules makes a separation process predictable.

The ChemAxon software will be used to create programs and methods capable of predicting the outcome of stereoselective reactions and also predicting novel organocatalysts. The software will be used with scientific workflow software (Kepler, KNIME) to couple quantum mechanical transition state calculations (Gaussian03) with the library generation/fragmentation abilities of the ChemAxon software to suggest new organocatalysts with higher enantioselectivity.

CADD on TCM fomula

Our lab will use your software: 1. bulit the pharmacophore 2. virtual screening the drug. etc.

We work on transport of Vitamin B12 and its analogs in E. coli. We use structural biology and other biophysical methods to decipher the transport mechanism of this essential cofactor. We want to manipulate and depict these small molecules in our figures and evaluations empahsizing different chemical properties. We would like to use your software to better understand and visualize the base-on and base-off states of Vitamin B12 and its analogs.

Considering as a possible alternative to ChemDraw for use in our Computational Chemistry Lab and use in Intro to Organic and Inorganic Chem courses.

Preparing lecture, quiz and testing materials

Synthesis and evaluation of molecules in drug discovery

providing tools to do structural searches to students trying to implement databases in day to day research

This software will be in particular used to calculate molecular properties, such as protonation, partitioning, charge, and so on.

I am working with semiconducting polymers. I would like to use the software for mainly preparing lectures. It will also be useful in writing papers

biochemical profiling

Your programs will be used to investigating reaction ability of molecules and ways of reactions, calculating structure constants and parameters. We works also with products of aldehyde\’s condensation, halcons, sulfons. Also we will glad to use your tools in education in different themes.

The specific teaching / research aims are tied to what I learn about the applications when testing them. The general teach / research aims are related to ensuring that students (undergraduates) are exposed to contemporary tools often used to tackle science problems.

Research Application: Database Docking and Pharmacophore Modeling Target Proteins: 1) T. cruzi DHFRTS; 2) Vaccinia Virus Proteins (dUTPase, UDG, TK)

Education of chemistry students in our nature science classes

The ChemAxon products would be used to create a database of chemical compounds as well as molecular descriptors for use as input in Data mining.

I wish to use the calculation options of the program. I use the program mainly to sketch molecules and molecular assemblies for material science applications.

Use in surface mass spectrometry and atomic force microscopy research: structure drawing, fragment scission, molecular areas, …

Metabolite and protein structure analysis

We plan to use the software as part of our efforts to develop some new approaches to libraries of peptidomimetics. In particular we are interested in the calculation of properties, and the enumeration of structures.

Rsearch in QSAR studies

Need the programe to construct geometrically viable chemical structures of proposed inhibitors which i aim to use in molecular docking studies in order to compare to crystal structures of existing inhibitor-enzyme complexes and predict and propose new chemicals.

Primararly, to use with the HierS implementation by GNF

Assist academic researchers in carrying out high-throughput screens of chemical libraries

Investigate using JChem on top of a relational PubChem database. Learn about cheminformatics software development in Java.

Development of new kinase inhibitors

designing a user interface for pubchem using jchem.

Our research group utilizes structure-based drug design to develop ligands for novel protein-protein and protein-dna interactions. We are very interested in using the quantitative tools available to parameterize these ligands and correlate cellular penetration, binding affinities and drug-like properties. Academically I teach a course on drug discovery and development, which focuses on many aspects surrounding drug discovery. We would like to use this software to evaluate physiochemical properties of compounds discussed.

Our most immediate use will be in evaluating a web-based structure drawing deployment for our Department. This will be open both to our researchers and our students.

Organic chemistry

Synthesis and characterisation of potential DNA-Intercalators. The software is intended to be used in managing of structures and characteristic data of the synthesized molecules an the calculation of values like logP… Students will be trained in the usage of new software products, leading to an economization of their work.

We want to implement ChemAxon chemical database machinery as main architecture in our institution. It will be used primary for teaching and optionally for research studies.

We are developing an open access educational-academic drug discovery process for developing world diseases. We call it \”Distributed Drug Discovery\” (D3). We have demonstrated that through D3 students in Russia, Poland, Spain and the US can make potential drug molecules as an integral part of their education. A critical component of D3 is generating open access virtual libraries based on the simple chemistry these students can carry out with inexpensive equipment. The virtual libraries will then be analyzed with developing world disease computational models and the selected set of candidate molecules synthesized by our distributed network of students.

Aspects of use. Pharmacophore analysis, Screening for similar compounds, possibly clustering, generation of molecular descriptors, possibly fragmenter and possibly metabolizer. I\’ve docked the tanimoto 0.6 drug-like ZINC compounds and the NCI diversity set II to the Nef proteing of HIV-1. I am currently in the processes of generating peptides using molconvert that are also to be docked after filtering. The working title of my research is Rational Drug Discovery by using Computational Methods targeting the Nef protein of HIV-1

I am researching a protein related with breast cancer and we would like to know the complex structure with the protein and inhibitor. Then I would like to use the software to draw the pictures of inhibitors..

I would like to use Marvin Calculator to check the properties of organic molecules that I want to screen on a protein.

My research interests includes a)Natural product chemistry b) microwave chemistry c) green chemistry d) organic synthesis Teaching involves, teaching first and third year students.

Use generatemd to generate structural fingerprints of compounds in screening library. This enables me to accelerate docking screens by using an iterative strategy where each new set of compounds to be docked is structurally related to high scoring hits from previous round. I have used this approach in the screening for inhibitors of IgE-IgER interaction, which is a target in asthma. The work has been funded by AsthmaUK: \”October 2008-October 2011. Structure-based discovery of small-molecule IgE in ibitors. Asthma UK. 3 years £199,765. Prof Brian J. Sutton, Dr Mary D. Holdom, Dr Andrew J. Beavil and Dr Gareth Williams\” This work will lead to publication and ChemAxon will of course be acknowledged

My research interests are mainly the computer aided drug design, more precisely the structure-based drug-design. The Chemaxon tools are of choice for my postdoctoraal project for managing the chemical libraries with JChem and IJC but also for simply browsing large SD files or editing with MarvinView and MarviSketch.

Draw Chemical Structure in 2D or 3D for paper

Using a variety of chemical informatics tools to support teaching.The most important content is to assist computer-aided drug design.The Markush search is point too.

- Preparation of the lignads - Prediction of the chrateristics of the materials - Preparation of the receptors

research in crystallography

Design and edit small compounds do study the affinity and bindig behaviour to potassium channels

We are an academic instituion focussing mainly on cancer research. One area of our research interest is targetted therapy. As a part of our reseach methodology, we tried to find out small putative inhibitors against validated molecular targets in breast and prostrate cancer. For the same we carreid out Virtual screening of a colelction of about 5 millon compounds from Ambinter database. We need to acess the chemical details of those compounds and its lipinski parameters . Visual inspection of those compounds and chemical properties of the same also have to be studied. We need Marvin tool to view and analyse the structure. Along wit thta we are planning to calculate structure properties using Calculator Plugins. It would be a great help if we could acess Metabolizer to analyse metabolic pathway stabilty prediction.

I work with metabolites and I would like to apply enzymatic reactions on some data, since I am interested in understanding better the metabolite space.

Evaluating aims

Bioinformatics Web Application. The Application we are developing now will be free available for public. So please give us a license that has no limit on access per minute.

To use the molecules to model adsorption

I am teaching several graduate level classes in the Biochemistry, Structural Biology and Virology Courses (BMS504a, BMS632, BMS653, BMS553) on enzyme structure/function, drug design, discovery and resistance. I want my students to understand and appreciate 3D structure, (Q)SAR and other critical requirements for drugable lead compounds and potential drugs. In the Biochemistry and Virology classes the students will be given several examples of polymerase/HIV RT inhibitors (nucleoside analogues and allosteric compounds) and they will study and evaluate the different properties of these compounds.

Through the Reactor, we plan to create a massive set of linked and fused organic molecules. Our objective is to have a set of smiles files which could later turn to 3-D for calculation of its properties. The objective is to have a massive library of molecular properties.

1. Automatic pKa and LogP and MW calculation for given set compounds to show the power of chemometrics to students 2. For research: 1) Routine Chemical structure retrieval and drawing for publication 2) Chemical databasing 3) Analysis of chemical database for supporting our acedamic research departments in our institute.

I\’m a student at the RWTH Aachen University and would be interested in a free academic license for the calculation plugins for my studies. If necessary I can provide a enrolment receipt. Please note that the street information provided above is my own flat.

I would use JChem to include structures in Excel files for the development of property prediction tools.

Simple molecular graphics for use in publications and (eventually) thesis. Will need basic functionality comparable with chemdraw, for example, converting name to structure and vice versa.

descriptor calculation

will use for presentations

I am interested in using the method for both graduate teaching and my own analyses in computational chemsitry, and ADMET modelling. I have published these papers recently in the field and would like to use ChemAxon methods in my research where appropriate. Gleeson, M. P. and Gleeson, D. QM/MM As a Tool in Fragment Based Drug Discovery. A Cross-Docking, Rescoring Study of Kinase Inhibitors. J. Chem. Inf. Model. 2009, ASAP article. Gleeson, M. P. and Gleeson, D. QM/MM Calculations in Drug Discovery: A Useful Method for Studying Binding Phenomena? J. Chem. Inf. Model. 2009, 9, 670-677. Gleeson, M. P. Generation of a set of simple, interpretable ADMET rules of thumb. J.Med. Chem. 2008, 51, 817-834. Gleeson, M. P. The importance of the domain of applicability in QSAR modeling. J. Mol. Graph. Model. 2008, 26, 1315-1326. Gleeson, M. P.; Davis, A. M., Chohan, K. K., Paine, S. W., Boyer, S, Gavaghan, C. L., Arnby, C, H, Kankkonen, C., Albertson, N. Generation of in-silico cytochrome P450 1A2, 2C9, 2C19, 2D6, and 3A4 inhibition QSAR models. J.Comp. Aided Mol. Des. 2007, 21, 559-573. Gleeson, M. P. Plasma protein binding affinity and its relationship to molecular structure: an in-silico analysis. J.Med. Chem. 2007, 50, 101-112.

To enhance high throughput virtual screening efficency, the modules of ChemAxon will be used to calculate som properties of the small compounds to filter out the un-drug-like molecules, then the screen module will be a good hits enricher for large-scale database. Our group has been licensed to access pipeline pilot and Knime, on which JChem and Marvin are suitable to integrated as workflows to perform above manipulation.

Drawing chemical structures to provide slides for students.

I am a teaching assitant. I need to draw some chemical structures in order to give a vivid lecture.

Structural studies of biomolecules

Use to improve IRIC chemical collection library

In Silico Strategies to identify novel compounds on MRP-1 - Pharmacophore-based drug discovery - Ligand Screeing - Databse mining

The software is a tool which supports a gain in the understanding of chemistry within biological systems. The uses of this software are focused on visualizing molecular structures in order to better comprehend intermolecular dynamic through conceptual modeling.

To draw chemical structure

For educational purposes, like visualization of molecules

A viewer is needed to visualize sdf chemical structure files for a chemical screening project.

Small molecule visualization REDEC

We are a small research group running drug development at the lead discovery state in an academic setting at the division of pharmacy in Åbo Akademi University. I recently moved here and saw the need of managing our small compound collections in a fashion that could store also experimental data and calculate partition coefficient etc. I\’ve tried instant JChem and Marwin draw and I\’m rather impressed with the software. Now I\’d like to test the plugins within the database and perhaps create a database in mysql that we could share.

production of combinatorial libraries for solar energy research

Mainly for teaching. Because I have not used your software before, I would like to take this opportunity to evaluate it as well. I can envision using the property calculator and possibly the library enumerator for some research project, if it fits my needs. I can actually let you now as I move forward and start using it. If I use it in the lab, I would like to have my students use it. But for now, we have never used it as mentioned above.

This software will be used to calculate pka values of amines targeted for crosslinking.

Planning to use Molconvert to generate IUPAC names for SMILES strings in order to make molecular information available to the chemistry community at large.

We intend to use the software as part of the Chemistry and Computational software we are installing in our Chemistry Computing Lab. We would also like to use it as an interface to an implementation of the chemical inventory databse software from http://www.chemicalinventory.org.

The software package will be used to evaluate some compounds that may or may not interact with some protein targets.

The SMDC is an academic screening center at the University of California San Francisco. We intend to integrate JChem Base with our existing chemical inventory database and nascent web application, and use Instant JChem to analyze hits and provide a foundation for medicinal chemistry.

Identification of antifungal potentiators.

For use in library design with NIH Pilot Scale Library synthesis project (PI: Prof. Scott E. Schaus)

I need this tools specially for performing energy minimisation of small molecules.

I plan on using it to gain a better grasp on organic chemistry by using it as a study aide for Organic Chemistry.

Teaching: medicinal chemistry – application of software in the design and development of therapeutic agents Research – design and development of therapeutic agents

Comparison Study to evaluate currently available applications

Plan to use the logD and logP calculator in the development of some new compounds that function as enzyme inhibitors.

The software will be used as a teaching aid in an undergraduate drug design course.

The software will be used as support for lectures in chemistry in the enginery school ECPM (Ecole de Chimie Polymère et Matériaux) of the University of Strasboug. The software will be installed in a computer room of 25 computers. This is accessed only during lectures. Computers of this room cannot be used from outside the room. All installation and license files are seccured by the informatic departement.

Phytochemical biodiversity database Metabolomics

thanks

The ChemAxon software will be used to develop applications for chemoinformatics and pharmacoinformatics analysis of physical properties involved in mediating bioavailability. The development of these applications will take place within a drug discovery training environment and can be used to educate trainees in the area of chemoinformatics.

The tools would be used for various aspects in drug design and force field parametrization.Ranging from chemoinformatics to fragment based design of molecules. Various Marvin tools would be utilized at various levels in the research work.

The research aims the elucidation of reaction mechanisms, so tools as charge calculation, pKas etc are usefull

We are setting up a College-wide centre for drug discovery. We need a chemoinformatics system to cover registration of compounds, obtained both commercially and from Imperial\’s chemists, as well as tracking compound testing, carried out in our screening laboratory. We supervise a number of PhD/MRes students whose aim is to discover new drugs for a wide range of clinical implications and they will all be taught to use the software. Imperial also runs a 4th year undergraduate course in Medicinal chemistry.

The software will be used for drawing molecules for research purposes.

Research includes host-guest interactions.

teaching a chemoinformatics class to undergraduate students

Our research mainly focus on discovery of G-quadruplex DNA binder via high-throughput docking, the hit compound can be deriviatived by using ChemAxon.

Computer Sciences Computer Chemical applications

learn and teach structure and other information easyly

Program will served for research purposes in the area of new drug disovery where is need to provide and calculate different molecular descripors which will be necessery for assessment of biological activity of new compunds in different environment.

I will be teaching an organic chemistry second year chemistry class this year. I am looking for a program that will help draw organic molecules for use in lectures and tests.

Investigations in pharmacokinetics, modeling, structure analysis and prediction. Teaching my students to use chemaxon software for db structural analysis coupled with HPLC-MS and GC-MS data

draw chemical structures for lesson plans

Study chemical behavior in the environment

preparing molecules for MD simulations

Use of MolConvert in a freely available web implementation of the newly created Reaction InChI software.

help students learn organic chemistry

structural based drug design teaching

Simultaneous determination of heavy metals in waters employing optical sensors and multivariate calibration

to manage new compounds and there informations

Our project evaluates quantitative structure-property relationships (QSPRs) for predicting fate of organic compounds in conventional wastewater systems. The ChemAxon utility will be used for estimating input parameters such as pKa and logD.

Use in Biochemistry 1 (CH339K). May add functionality to website as well as using in demonstrations and display.

Drawing small molecules for publication, pertaining to our research on secondary compounds in lichens

Molecular modeling of synthesized agents

My reasearch topic is synthesis and analytical studies of schiff bases.I need this software to draw some structures.It really helps me.

Teaching students in Analytical Chemistry.

Teaching – for use by students in MCMP 205 Organic Chemistry and MCMP 625 Grant Writing Research – design of modified nucleic acids and modified nucleoside analogues; self-assembling molecules.

We are screening libraries of small molecules for inhibition of Mtb. We want to search for similarities between hits across libraries, calculate physical properties of any hits and compare structure and physical properties of hits vs non-hits. We would also like to compare our compounds of interest with published compounds.

Teaching students about methods to relate chemical and physical parameters to experimental observables, and how knowledge of chemical structure can be used to predict properties.

Teaching: Physical Chemistry laboratory development. The new laboratory will combine spectroscopy, HOMO/LUMO calculations, and database searching to simulate QSAR analysis. Research: The development of a dye-sensitized solar cell database which will be made freely available. This database will allow the evaluation and selection of DSSC\’s for particular uses and further development.

Student use.

computer aided drug design and cheminformatics

Having taught chemistry previously, an in-depth sketch and modeling program is integral in the success of some students in the class who need visual representations of what we are learning about. Chemistry is very abstract and a complete modeling program helps lend some concrete images to the students as they learn the material. I would implement the program in the classroom during instruction, laboratory experiments, and personally when preparing examination items. I would also use it to provide a computer-generated study guide of molecular structures to organic chemistry students.

Screening compounds

The software will mainly be used to generate the possible tautomeric forms of a database of biologically active molecules at various biologically relevant pH\’s. This database is being created as a part of my PhD project and once complete, will be screened against protein models created using other software programs in order to predict possible protein-ligand interactions. Determining the predominant tautomer at specific pH\’s will be very important for obtaining relevant docking results, but unfortunately the software program that will be used for the docking does not generate these tautomers, and as such it is necessary to gain access to another software program that will do so.

we are working on inhibitor design for sars cornovirus. we need LibMCS tool for clustering our ligands

We would like to evaluate JChem for use in studying the evolution of enzymes and their substrates.

for demonstration of software to students as an aid to future research programmes

=> To work on MolFragment for fragmenting molecules => Performe clustering using MolCluster => To work on Descriptor based screeing => Used by researchers and faculties

Research on cancer therapeutics

The software will mainly be used to evaulte pKa\’s of small molecules used for docking and other applications

Medicinal Chemistry classes for Pharm.D. students. Update: I have used this software through the ChemIDPlus Advanced interface for the past two years to help students understand pKa, log P, log D, and microspecies of various drugs. I would like to renew the license for another two years.

Introducing 2nd year chemistry students to chemistry software that can be used to solve chemical problems.

Visualize compound structure and information prior to campain screens. Be able to read ChemBioNet data base.

cheminformatics, and computer aided drug design descriptor calculation, strcture search

Dyes adsorption on to various adsorbents including activated carbon, chitosan, peat and bone char. The software will be used for the drawing of the dye structures, determination of molecular dimensions and pKa.

I am doing research in insilico prediction of metabolism prediction. for that purposes i have a list of compounds name(around 500) with IC50 values, i would like to get structure to develop QSAR model. best regards nathan

To build 3D structure of chiral molecules，and molecular mechanics calculation and molecular dynamic study.

The programs will be used for teaching undergraduate classes at the Department of Organic Chemistry. Moreover, it will also used for academic research at the graduate level.

Quantitative structure-activity relationships of peptides

I\’m working on sirtuins. I would like to draw the chemical reaction of sirtuin activity.

A series of aryl beta- hydroxy esters, which are important chiral synthons for synthesis of various pharmaceuticals and nutraceuticals were experimentally shown to get deracemised in the presence of Candida parapsilosis .Our study is to ananlysis the binding abilities of Candida parapsilosis with different \’S\’ group of beta()- OH ester .In order to understand the difference in preference of the substrate we used the target based study (ie) Enzyme-Substrate docking studies Target based studies includes homology modeling of the enzyme and subsequent enzyme-substrate docking studies. Docking reveals important interactions between the binding site of the enzyme and the substrate that may be fundamental in catalysis. Target based studies indicate that the preference of the yeast towards aromatic esters could be due to the cyclic structure ring of the substrate which was able to form the hydrogen bond with some Amino acids. The stereospecificity of the organism towards the ‘S’ enantiomer could be explained based on the prochiral orientation of NAD(H) which was found to be on the re face of the keto group thus delivering the pro-(R) hydride to the carbonyl group resulting in ‘S’ enantiomer.

We need an easy way to convert 2D molecular formulae into 3D structures…

By using the program, special presentations will be created for the students in teaching pharmaceutical chemistry. The students will be tought using to prepair their own presentations and dissertations.

To calculate the number of hydrogen bond acceptors/donors, MW and logP of a number of different compounds.

Using as cheminformatic tools for catalog and diversify molecular database. As for teaching, In the topic of \”CADD\” in Advance course for pharmacy students and MS. (Pharmaceutical Chemistry)

I will be using Marvinsketch as part of ACE Organic for homework problems in my Organic Chemistry I and II courses and would like to use the Marvin package of products during lectures to teach the students how to use Marvinsketch so that I can develop more advanced problems in ACE Organic and eventually move to online exams.

I\’m working on the synthesis and structral study of mesoporous/microporous materials, and this software is very helpful for the research, not only for drawing the 2D and 3D figures for the molecules and the framework structure, but also I can use it for the topology analysis, finding conformers, surface area, etc.

I teach chemistry from analitycal to physical chemistry.

polymer material science

QSAR research of persitent organic pollutant. Demostrate molecular structure in the class.

I am the IT person setting up the PC\’s in the Labs to teach Chemistry.

We would like to use ChemAxon software in teaching for chemical visualization during our practical courses.

Structural Biology

Perform computational chemistry support to several medicinal chemistry projects in drug design ongoing in the institute, specifically computer-aided lead discovery and lead optimization.

The software will be used mainly for comparisons of protein binding sites and small molecules. In particular the software \’Fragmenter\’ will be used to divide a small library of chemicals into fragments.

Development of original worksheets such as organic chemistry, and other assessments. Chemical structural labs and illustrations of molecular dipole. Using the space filling drawings to help students get past the textbook.

Conformers treatment, logP calculation

USE IN THE STUDY OF LOW DIMENSIONAL STRUCTURES

Impact of hapten molecules on electrophoretic mobility.

Our research interest is the synthesis of new compounds with novel chemical bonding such as multiple-bonds between heavier main group elements from a viewpoint of fundamental and material chemistry.

We are working on the problem of Drug-DNA Interaction using spectroscopic and molecular modeling techniques.

Studies are focused on organoselenium compounds and their application as antimicrobal and antivirial agents.

Undergraduate use

antidiabetic

cheminformatics, chemical structure properties calculation, structure visualization

Doing research on valsartan tablets

My research is in the field of thin polymer films for use in surface functionalization. I work in collaboration with materials scientists and organic chemists to develop novel polymeric coatings that can be applied for templating, surface assembly of nanoobjects, and biointerfaces. I will use chemaxon drawing software primarily to make drawings for presentations and internal written reports. The software might be used for in preparing future publications.

I want to use your software to prepare computational models for DFT and MM…

to carry out computational study to correlate thermo optic coefficients of polymers and their hybrids.

Environmental fate of antibiotics. Marvin software used primarily for calculation of logD of antibiotics and a to a lesser extent for calculation of other chemical descriptors e.g. molecular charge, H-bond acceptor/donor.

I would be using this to help my understand of organic molecules for work in Dye sensitized solar cells, as organic dyes will have to eventually succeed the platinum series organometallic dyes used currently.

I am especially interested in the combination of ChemAxon software with the JChemExtensions in KNIME, because KNIME is used extensively in our working group for setting up of eg virtual screens and dockings and ChemAxon tools seem to me as very useful additionaly option.

I take Medicinal chemistry course this semester. Our supervisor introduced us to use this software.

Research, because of the Bachelor of science in chemistry.

The program will be used to sketch and view molecular models and make graphics in an organic and biochemistry lab to help with visualization.

I\’m a Master Student in physics applied to medicine and biology and my work is related to photochemistry reactions in Photo-dynamic Therapy. The Photo-biophysics Lab (http://dfm.ffclrp.usp.br/fotobiofisica) makes research using different optics technicians. In our team there is two Full Professors (Prof. Amando Ito and Prof. Iouri Borissevitch) and one Research Professor (Prof. Luciano Bachamann). This software will be extremely important to our research to study different chemical parameters.

I wish to use the software in QSAR studies as well as virtual screening against a set of kinase drug targets. My hopes are to find novel structural lead compounds.

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I perform organic chemistry. Chemaxon is used to help predict conditions required for novel reactions based on physical predictions. e.g pKa

Use of 3D Homology Modeling and Virtual Screening Technology to Discover Anti-JC Virus Drugs In recent years, structure-based virtual screening technology has emerged as a powerful approach to rapidly identify novel inhibitors of enzymes and protein-protein interactions. As an illustration of the potential effectiveness of this approach, we quote the work of Liu et al (Liu, Z.M., et al. J Chem Inf Model, 2005. 45: p. 10-17), who sought to discover non-covalent inhibitors of the SARS coronavirus 3C-like proteinase, and performed virtual screening of 230,000 compounds. Of these, 40 compounds with a high docking scores were purchased for biologic studies, and 3 were found to inhibit the viral enzyme. We hypothesize that anti-JCV drugs can be discovered by screening chemical libraries for compounds that can bind to VP-1 and interrupt the interaction between the intact virion and its host cell receptor. Our approach to drug discovery envisages virtual screening of a library of approximately 5 million compounds from the Maybridge HitFinder, NCI, and Zinc databases for binding to ligand binding pockets on VP-1. This virtual screening will be performed using three dimensional homology models of JCV VP-1 bound to its receptor ligand. The top 50 scoring hits will be tested directly for their ability to inhibit JCV virus replication in cultured cells. Structures of compounds with promising anti-viral activity will be used for a secondary virtual screening, which will generate another focused set of compounds possessing pharmacophoric features of the initial hits. This second set of compounds will again be evaluated for their effect on JCV growth kinetics in cell culture.

It will be mainly used for, 1. Structure/scheme drawing 2. Prediction of compound properties 3. Managing my own database of a compound library which I synthesised to be tested in vitro 4. 3D Visualization when applicable 5. Managing Excel sheets which embeded structures

I will use these software for training of students in analytical chemistry. And some calculation packages will also help me to do some fundamental research.

Edit and vizualized chemical structures.

Database for chemicals in the lab

1st year module on Frontiers in Chemistry, featuring a couple of lectures on cheminformatics

I would like to try teach myself in generation/operating in molecular descriptors.

Drawing with the sketch tool, alogn with use of the charge and polarization tools, logP and logD used in the context of teaching separations (ex. chromatography). Other uses may arise as I gain familiarity with the tools.

Data and structure visualization

I do research with antibody engineering

I\’m currently working on an (non-profit!!!) german manual for teachers and pupils to work with Marvin Beans in schools as part of my final paper. This includes basic learning units for the program, lesson examples, examples on how to use it most effectively and what purposes it may be good and appropriate (for schools) or not so good. To perform this I already got one license key a while ago, but I am currently trying to document all necessary steps to get and license Marvin Beans. I\’m sorry for that extra work for you, because of this licence approval.

organic chemistry

Structure viewing, editing, drawing and stereoisomer generation in a ligand-based virtual screening project.

Robotics chemistry lab

Managing and searching structural databases. Virtual screening protocols. Calculation of molecular properties and descriptors.

draw structures of drugs being evaluated in research for use in presentations and publications

For use in computer-aided drug design research.

I need this plug in for my assignments in ace organic

The software will be used for teaching materials for Medicinal Chemistry course offered by the Faculty of Pharmacy. The software will also be used to calculate certain descriptors for drugs evaluated in our laboratory for academic research purposes.

Metabolomics and chemical biology including QSAR

Il use the logiciel in organic chemistry and inorganic chemistry

The potential usage of ChemAxon software includes descriptor calculation for QSAR, molecule structure management and standardization, excel management and database management.

In order to calculate different chemical properties of different chemical compunds, the chemaxion products will be used.

I am a student trying to teach (myself) organic chemistry.

It is intended that this software will be used for creating chemical reaction schemes for use in presentations and publications

hoe to device new techniques in teaching and educating my students to adore scientific material. regarding i need the software in my researches to improve the quality of my researches to the approved grade

Presently i am actively involved in QSAR analysis of some Anti-HIV agents. These tools will help me to aid some more and good results which will be published.

I use MarvinSketch to draw drug structures and view them in 3D. The software is useful for studying stereochemistry and conformational analysis.

The department of Chemical Biology in the Institute for Medical Biophysica and Biochemistry at Karolinska Institutet is a non-profit, national academic research facility dedicated to education and assisting academic groups in the Swedish research community with access to state-of-the-art tools for small-molecule research and development. Core capabilites include Assay Development, HTS, Biophysical and Physiochemical characterisation, and synthetic chemistry optimisation. It is hoped that the centre will aid in the development of high-quality chemical probes for unraveling the underlying complexities of biomedical science, thus aiding in developing innovations and new therapeutics.

Our research is focus in the optoelectronic devices. We are using polymers and organic molecules. We will like to try to understand better the chemistry and to write in the proper way

I teach small-molecule conformational analysis in a chemical biology course. I would like to encourage students to look at their chemical inhibitors in 3D and to understand their conformational preferences using the Marvin Conformation Plugin, among other plugins.

Our academic research group would like to utilize the ChemAxon software in our drug discovery programs.

Laboratory of Molecular Modeling and Design was established in September 2004. Our research mainly focus on computational simulation of biological complex system and the computer aided drug design. We have cooperated with many other groups in discovering and design drugs on the anti-virus, anti-tumor, anti-snail fever, nervous system disease and metabolism related diseases. We also work at developing drug design methods, including database construction, pharmacokinetic properties and toxicity (ADMET) prediction and multi-target drug design.

Calculate the properties of compounds for screening purpose.

Machine learning and kernel methods to predict molecular properties in large scale. The marvinbeans package is useful to compute features of the molecules to make the separation of molecules possible.

molecular modelling, stucture-activity relationships, docking and scoring

want to determine the logD, pka of the compound on different pH

Teaching: Part of PhD program in Med Chem Research: Inhouse chemical database, including small molecules, natural products and modified peptides

We are researching about Molecular Geometry Optimization and we want to use GeometryPlugin for calculating angles and also dreiding energy.

I will be exploring the various tools of the software package in order to eventually apply it for molecular modeling and quantum calculations in future projects.

I intend to use Marvin to help me to evalvuate and characterise \’hit\’ obtained from my virtual screening experiments and also in their lead optimisation.

Used in teaching of AP senior high school classes

I\’m interested in mostly in synthetic methods in organic chemistry and physical organic chemistry.

calculation organometallic compounds

Data mining, QSAR and molecule visualisation

Modeling of small ligands for development of molecular dynamics forcefield parameters.

Studium, Visualisierung von Dateien

I am to employ the Academic Package to my PhD research in Zurich on DNA-encoded chemical libraries and for the evaluation of small molecule libraries and medicinal chemistry projects. Please find a more detailed research description online, at Buller, F et al., BMCL, 2008 and Mannocci et al., PNAS, 2008.

Drawing and exporting molecules for parameterization in gaussian.

The Vienna University of Technology offers several fields of study. They are offered bachelor and master as well as postgraduate doctoral programmes. I would like to use the ChemAxon products only inside of our institute, install and try it out in my laptop, how they are applicable for the daily work. Administration, visualization and first at all chemical calculations are the main areas. I have also interest at Reactor and at JKlustor. At the beginning I would like to install IJChem only in my laptop and don´t want to give acces for other persons or student, later may be have interest at the base version however only for students, who are active in our Institut, so that they finish the thesis (diploma) more easily. Pleae tell me how and where can I download Reactor, and JKLustor because I can´t find them on the ChemAxon home page.

Research in sulphonamides with pharmaceutical activity

I would mostly like to generate molecular properties for QSAR models

clustering of small molecules inhibiting enzyme activity

computational

I would like to calculate the charge of human metabolites at various pH. More generally, I am interested in chemoinformatics tools which can be used as part of mass spectrometry software pipeline.

medicinal chemistry course requires becoming familiar with this software

1. Teaching aim We are trying to make a course for the Pharmaceutical Department of Gadjah Mada University, basically the course is about Molecular Modeling. We try to introduce to the new student about how easy and useful it is to use the free softwares available on the internet, and the we\’re gonna direct them to study Computer Aided Drug Design (CADD). 2. Research Aim Our research group is trying to combine the CADD, Pharmacology and Organic Synthesis to create a new potential drug. We\’re using Marvin to build some structure for the virtual screening and to manage our compound library.

Characterization of substrates and inhibitors of mammalian drug transporters.

Mimetics of coiled-coil motif by terphenyls

In the last two decades surface science techniques have decisively contributed to our present knowledge of thiol self-assembled monolayers (SAMs) on solid surfaces These organic layers have been a challenge for surface scientists, in particular because of the soft nature of the organic material and the complex physical chemistry involved in the self-assembly process. This challenge has been motivated by the appealing technological applications of SAMs that cover many fields of the emerging area of Thiol-capped metals have a wide range of technological applications especially for building systems by bottom-up methods. In most applications a detailed knowledge of the system at the molecular level as well as the stability of the organic film during exposure to ambient conditions and/or to electrolyte solutions is a crucial requirement. This project investigates the self-assembly process, surface structure, adsorption sites, defects, thermal and electrochemical stability of tiols monolayers (SAMs) on different metal and semiconductor surfaces (Au(111), Ag(111), Cu(111), GaAS(110), Ni) prepared from the liquid phase and gas phase. STM, XPS, GIXRD, ISS-TOF, and DFT are used to characterize the monolayers.

Teaching of Chemoinformatics. Exercise classes for structure representation, 2D visualization, 3D visualization

My research advisor has recently jumped on the technology bandwagon at my behedst. We have just completed a COMPLETE electronic catalog/online database for all of the chemical reagents found in the lab, and this is the next project I have been tasked to handle. What we\’re looking to do is to utilize this database software to log all of the compounds that we\’ve synthesized in the chemistry lab and use that in conjunction with the data generated and stored in our soon-to-be-implemented CERF database. The hope and aim is to increase a more real-time and easy sharing of both chemistry and biology data to generate more papers in a more timely manner. We are on the cusp of some REALLY interesting chemistry and biology publications, this software will greatly aid our efforts by de-cluttering and streamlining our operation.

The software package would used for illustration of organizing chemical information and prediction of physical properties for university student in the department of pharmacy and pharmacology.

To learn to handle databases

Teaching 14-19 science. It will be implemented throughout the GCSE/KS3/AS/Alevel parts of the course.

I use it for the organic sections in general chemistry as well as in tutoring organic chemistry.

Our research is essencialy focused on the structure-based and ligand-based drug design. It\’s really strictly required for us calculated phisical and chemical parametres such as logP, logD, TPSA, pKa and so on, at least it\’s deeply essencial also the possibility of managing these great amount of data. For this reson we would like to have the licence for Marvin package.

chemistry research

To do assignments for my class in Medicinal Chemistry (instructor: prof. A. Doemling), I have to use ChemAxon Reactor and Instant JChem software.

I am master student doing some introductory research in drug design. I will primarily be using the msketch to extract information from published research.

Teaching in clinical pharmacokinetics of drugs. Research on therapeutic drug monitoring.

We will build an in house data base of all compounds synthesised in the department including biological data; this can then be easily shared. Students will use JChem for Excel to generate data sets and run some simple correlation analysis in the framework of the Pharmacoinformatics PhD curriculum.

I am a graduate student working in synthesizing medicinally active compounds

I\’m using it for classwork in my different pharmacy classes. The program is 4 years long.

Student in Orgo.

Tools for quantum calculations (converting of mol files etc.)

Will be used for organic chemistry class learning

To write a chemical constitutional formula in the report.

My research topic is investigation of fate and transport of pharmaceuticals in aquatic environment. For my research, the chemical properties of pharmaceutical are key parameter. For example, hydrophobic pharmaceutical can adsorb on organic surface in environment and octanol-water partition coefficient (log P) of pharmaceutical is import parameter to estimate transport of pharmaceuticals in water. Academic package of ChemAxon will be used two main purposes. First, estimation of octanol-water partition and distribution coefficient (log P and log D) will be calculated. The hydrophobicity of pharmaceuticals depends on pH of water and the specific data of pharmaceuticals under different pH are not usually available. However, ChemAxon software (Calculator Plugins) can predict log P and log D based on the chemical structure of pharmaceuticals. This function of the software will significantly helpful to understand fate of pharmaceutical in aquatic environment. Second, metabolite of pharmaceutical will be estimated using ‘Metabolizer’. Pharmaceutical can be degraded in environment by microorganism. If metabolite products of pharmaceutical are known, detection and quantitative analysis can be achieved much easily.

Our group, the Center for Structural Biology, uses X-ray crystallography to determine the three-dimensional structures of proteins which are candidates for drug targeting. We then use this structural information and a combination of computational and high throughput wetlab techniques to screen for small molecule inhibitors of the protein. This application will be used to understand some of the chemical properties of our small molecule \’hits\’ that may be used as inhibitors.

We are setting up a team which will be working with fragment based lead generation. Jchem (and other chemaxxon software modules) is the best solution for managing the database of fragment and compounds as well as data from screens etc. In addition, the chemintelligence also is very helpful in predicting logP etc. This would be the main usage as it is right now. The honest answer is that I dont yet know the full scope of what the software can do, hence I belive it might be used for more applications when we have learned how to better use it.

This software will be used to prepare slides and handouts for classes. I will mention to the classes that I use an alternative to ChemDraw for those who are not interested in MS Windows and provide more information on request.

I will be teaching students organic chemistry using technology to help them understand the material. With so many useful resources available, I will be able to reach out to more students, enabling them to enjoy chemistry!

Modelling a protein-DNA complex and subsequent docking of compounds to the complex. Therefore, the ability of compound library comparison and clustering is a crucial step which needs appropriate software.

Calculation of small molecule properties to facilitate drug design

molecular design, screening

Organic chemistry use.

For general calculation of cheminformatics, such as pKa, majorms, structural frameworks, etc.

Cheminformatics

We will be using the software (esp. calculation of pKa profiles) to aid in the development of a purification method of dyes from plant extracts

The implemetation is for the following purposes: 3D viewing of proteins surface charge distribution of proteins polarizability of proteins

The library manages our campus site license to another chemical structure drawing software suite. We have many Mac users who are looking for alternatives to this product, since the software we license has very little in the way of Mac software and support. I don\’t do any chemical research myself, but I am trying to help users set up databases or use the structure drawing tools. I would advise our users to apply for their own individual ChemAxon academic license as I assist them with set-up.

Computational drug discovery. Protein-protein interactions and docking. http://structure.pitt.edu/

I am interested in evaluating these tools for potential use in my research & teaching.

use in the chemo/bioinformatics field for study of protein-ligand interactions.

just using the tools menu option to quickly access molecular properties, such as pka

Evaluation of molecules stability, reactivity and physico-chemical properties

To assist in the characterization studies of the biological activities of venoms, with the aim of seeking new approaches to the treatment of patients envenomations in Brazil.

We are studying the conversion of biomass, particularly cellulose, to fuels or chemicals. Currently we are studying pathways for the decomposition of glucose in different solvents. This research entails both experimental studies and computational chemistry.

Research aims: find preferred ligands for mouse olfactory receptors. Aspects of use: Drawing managing structures, computing physicochemical properties, converting file formats

Molecular Dynamics of protein Molecular Virtual Screening for new drugs

I have benefited greatly from using Marvin as a study tool for my organic chemistry classes, and would like to have access to the academic package so that I can have the extra plugins (such as the isomer plugin – would be very helpful to be able to check my work).

We want to use the Reactor program and its pipeline pilot component to build up our compound database.

Organic chemical modeling.

Physicochemical property prediction for natural flavonoid antioxidants.

ligand protein interaction

For the teaching of organic chemistry

Work on antioxidants in food systems. Teaching food chemistry and surface&colloid chemistry.

antiviral drug design under NIH funding

I am currently doing research with Dr. Alexander Doemling who has asked me to download this software because it will be necessary for my use in the future. I Currently am doing isocyanide based multi-Component reactions, and am coming up with a project of my own using MCR and looking at creating potential drugs. I need an updated license to use Jchem for excell

We are investigating protein and peptide structures by using NMR spectropscopy and perform medicinal chemistry after screening. Therefore students need to get familiar with the structure of chemical compounds.

Marvin Sketch will be used in the same way chemdraw is used. Creating structures for poster presentations and lab reports.

As part of the our project the goal is to identify drug candidates that inhibit selectively those dominant oncogenic mutants, that are driving the cancer while the wilde-type protein of that oncogene will not be affected. As one approach of this project the goal is to identify compounds from commercially available sources by a virtual screening appoach. For the handling and selection of input structures it is planned to use ChemAxons database Instant JChem.

Development of fragment-based screening methods. Database of a library of chemical structures. Handling of screening data. Possibly use screening hits to elaborate and synthesize more potent binders.

Organic chemistry research

the program will be used in academic research that allow the student to explore the different program tools. although give the student an idea f how important is the software and computing now a days.

Computational Drug Discovery

I have great interest in the field of computer assisted chemistry, but am particularly interested in synthesis design using the \”Reactor\”. I believe when combined with a 3-D molecule viewer it is easier to grasp the concept of why certain functional groups undergo some reactions and not others. This can be valuable tool that offers student chemists a different perspective than the traditional model kit. As ball and stick model kits are limited to one visualization electronic sources can plot out electrostatic potential maps, calculate charges and show resonance structures. As I said I\’m interested developing software as a learning aid with more potential than ball and stick models.

Use chemaxon library to develop drug design

Teaching and research in Computational-Organic chemistry. Conformation Tautomerism Resonance Acidity Basicity

Provide undergraduate and graduate students with a freeware chemical drawing tool of prefesional quality. Create on line inventories of reagents for academic laboratories

I would like to evaluate this app for teaching (Year 3). I have little control over installation of addins to general access machines so I cannot say if I will be able to use it widely. I will investigate the addin for our research.

A compound database will be established in our lab and the ChemAxon software were considered to be wonderful information managing soft. ChemAxon software will be used to administrate the structural formula, the chemical properties and the biological activity of the compounds.

Used in file conversion and in finding minimum energy conformers for docking experiments

Theoretical investigation of molecular crystall packing.

studying pharmaceutical chemistry

Para pesquisa e aprendizagem para futuras aulas de quimica e quimioinformatica.

this software is used in molecular modelling course to teach undergraduates . It also is used for QSAR research studies

personal learning

The department of Chemical Biology in the Institute for Medical Biophysica and Biochemistry at Karolinska Institutet is a non-profit, national academic research facility dedicated to education and assisting academic groups in the Swedish research community with access to state-of-the-art tools for small-molecule research and development. Core capabilites include Assay Development, HTS, Biophysical and Physiochemical characterisation, and synthetic chemistry optimisation. It is hoped that the centre will aid in the development of high-quality chemical probes for unraveling the underlying complexities of biomedical science, thus aiding in developing innovations and new therapeutics.

The department of Chemical Biology in the Institute for Medical Biophysica and Biochemistry at Karolinska Institutet is a non-profit, national academic research facility dedicated to education and assisting academic groups in the Swedish research community with access to state-of-the-art tools for small-molecule research and development. Core capabilites include Assay Development, HTS, Biophysical and Physiochemical characterisation, and synthetic chemistry optimisation. It is hoped that the centre will aid in the development of high-quality chemical probes for unraveling the underlying complexities of biomedical science, thus aiding in developing innovations and new therapeutics.

Use for teaching basic chemistry concepts to high school students

I\’m the director of the OWL project and we work cooperatively with the Chemistry department here on grant based educational research. We also work cooperative with Cengage Learning who license our software (and ChemAxon software) as part of the commercial OWL system. I have met with the ChemAxon team many times to discuss our ongoing relationship.

I aim to use the program to show my students VSEPR theory and molecular geometry.

Used to demonstrate models of various compounds.

Creation of molecular structures to teach Organic chemistry

Research in the area of amino acid transport and developing selective ligands as tools for biology research. The development of pharmacophores and conformational analysis is critical for this, as no x-ray is available for most of the proteins of interest.

Our research is about the calculation. Recently we want to do some reasearch about the organic reaction mechanism. The software can do the conformation search is needed. So we want to use this software.

developing a QSAR model, where the program will be used for calculating/developing descriptors. This is within the field of CO2-capture.

I need to see my chemical structures which are in SMILES, in excell where I could i have other columns like activity dat anad so on..

(not sure about teaching/research, as our case is none of them) We require a tool to calculate the chemical structure of a given compound at a given pH value. In particular, to bring the compounds we use in our reactions database (Rhea – http://www.ebi.ac.uk/rhea) to pH 7.4. So far, they have been normalized to their neutral form, with some exceptions. This will make our database more compatible to other resources. The use we envisage of Marvin calculator plugin(s) is one-shot, to make a global data transformation, and not for incorporation into any public web services.

Training/teaching and research in medicinal chemistry and chemical biology.

I am working on the Structure based drud design of anti-cancer agents.For which I need to perform several chemical structure generation and studies with MD.This package would be of real use to my research.

Tutoring undergraduate students in second year organic chemistry, the MarvinSpace program will be used to show small groups of students (in tutorial) the following concepts: 1) Charge distribution 2) Chirality 3) Cyclohexane conformations (Boat vs. Chair etc.) 4) Towards the end of the course, visualizing some larger molecules like polypeptides and polymers 5) The power of computers in predicting properties, like NMR spectra (chemdraw) and pKa\’s/isoelectric points (Marvin)

I am mainly doing MD simulations also teaching phd stuents.

antyHIV, integrase, QSAR/QSPR

generating structures of compounds

Data mining and QSAR modeling

ligand and protein interaction

I am teaching medicinal chemistry. In the medicinal chemistry course we talk about computer aided design stratagies and this will be perfect to be able to show the students a direct example. For research, I am interested in understanding regulation of proteins at cysteine residues and would like to be able to determine which cys residues in a protein have the lowest pKa\’s so I can implement mutational analysis on those first.

Teaching on master degree level exemples of descriptor calculations for QSAR. Software installed to a specific computer accessed locally. Research on drug/membrane interactions and molecular modeling.

To calculate logD values for the E. coli metabolome.

I\’d like to calculate polarizabilities of some molecule.

I am initiating a program in environmental chemistry and like to show the students the tools (such as acid dissociation constant, log P) can be modeled using your software.

I will be conducting seminars on the pharmaceutical industry with particular emphasis on medicinal chemistry and looking at aspects of leading finding and library synthesis, the ability to demonstrate, how to generate a library of compounds and tolook at the physical properties would be very useful for the students

I think ChemAxon will be very helpfull in my research since currently I´m working on the theoretical development, computacional implementation, validation and application of novel measures of chemical similarity.

study the interactions of Protein and small molecules

I am a student at UNCG and I am taking Organic Chemistry and using Ace Organic. When using ace organic it says I need a lisence from Chemaxon to use steroisomers,

K12 school – teaching children the basics of chemistry

polymer structure by afm

I am currenttly a chemistry teacher at a Federal University in Brazil and intend to use the software to increment teaching of compounds properties like acid/base behaviour. In research, we have a partnership with another federal (also from government and non-commercial) institution for development of drugs for neglected diseases.

Wish to use as learning aid

Using MarvinSketch for making presentations used in Medicinal Chemistry 1, Medicinal Chmeistry 2, Drug Biochemistry & Metabolism

This will be used for further understanding and use in Organic Chemistry.

LogP calculation, drawing

I will use the software to more accurately depict molecular structures to my students.

We would like to determine the polar surface area of siderophore molecules in order to make preliminary estimates about how they may be incorporated into a humic acid micellar solution. We will use this information to interpret future 19F NMR studies to see how incorporation into micelles changes siderophore conformations.

I will use this software to convert SMILES strings to precisely defined chemical graphs in an automated fashion. I will also explore the utility of this software for making calls from MATLAB and python to compute chemical descriptors.

Carbohydrate synthesis

Current research project is Molecular modeling (QSAR)

The software will be used to teach postgraduate students about chemical databases and their use at screening facilities. Some concepts about clustering and virtual screening will also be teached.

basic organic chemistry lab

The software will be used for my research on computational drug design. It will also be utilized for teaching in my course, Biomedical Physics, PHY 316.

I\’m studying about bio-activity of compounds in natural resources. I will use this app. for drawing these compounds in reports.

Chemistry

I need to make use of JChem java package for calculation of thermodynamic parameters with open source java classes that make use of certain functions from JChem.jar. My general work is about metabolome description/study.

Berechnung von pka-Werten

We require visualization and chemi-informatics software to support our research efforts in the chemical biology of DNA replication.

Bachelor theses

Conformer search

draw molecule to present different functions to student

The tools will be used by students in their diploma research work in the Kyiv University

We will use JChem for calculating physicochemical properties of small molecules, which will be used for creating SAR models.

Structure elucidation using NMR spectrscopy

Determination of physicochemical and pharmacokinetic properties of drug molecules.

Creation of scientific molecule libraries for screening purposes.

Would like to carry out sub-structure searching

Research into drugs against neurodegenerative diseases.

Teaching – Advanced Organic Chemistry lab Research – Orgametallic synthesis and catalysis

Our research group is a multi-disciplinary group working in lead optimisation based on the ADME properties of a range of compounds, targetting various medicinal targets. We would like to apply some of your tools within the JChem package to evaluate and manage in silico properties of our library of structures. The ultimate and hopefully publishable goal is to build models for predicting in vivo properties. Teaching applications will be limited to post-graduate students, who are likely to generate publications, but possibly not until after Thesis submission at the conclusion of their studies.

To aid my in tutoring my classmates

to work ace organic

We are investigating ways of using Marvinsketch with online tutorials. Students would draw structures in Marvinsketch and then copy the structure as a SMILES string to Blackboard for assessment.

I will use MarvinSketch as a potential tool for students taking organic chemistry lab courses.

Demonstrating the relationship between structure and function in biochemistry

My research involves analysis or virtual libraries with a special interest in heteroaromatic rings. I am also working on aspects of the druggability of protein-protein interactions.

determine of hydrophobiciti and partition of antibiotics

The software will be used in the teaching students that are attending the MSc in Drug Discovery course. This course covers the modelling of small molecules and evaluation of their confomational flexibility in respect to the importance for receptor binding. Also the determination and prediction physico-chemical properties is part of the course. In research, the small molecule – small molecule interaction will be studied and how that affects the physico-chemical properties.

evaluation period for: - modelling in chemistry (Licence to master) - molecular models buiding - 2D to 3D converter - structural optimization - conformational search for the moment, no sofware implementation is envisaged.

I hope to use this software to provide third year chemistrystudents with experience in the use of cheminformatics software. The software will be used for a minimum of two three hour sessions. The first session will involve the use of Marvin Sketch and the calculator plugins. The second session will involve the use of Instant JChem. I will be preparing procedures whcih will evolve as I become used to the software myself.

I will use ChemAxon for calculate pKa of compounds

Studies of new drugs and docking

New beta blocker synthesis

Software will be used to teach student about chemical structure and exploration of activity data.

Will be using it in my Pre-AP Chemistry and AP Chemistry classes. Will be used in discussion of covalent bonding along with molecular geometries of covalent compounds. Will use it to show Lewis dot structures. Will be using it to create 2-D and 3-D molecules for discussion in class. Currently learning what MarvinSketch can do. Would like to use it for showing chemical reactions and simple organic reactions.

First-time user; don\’t know yet.

We want to evaluate the program for using it in both research and teaching. Our research involves the synthesis and evaluation of anti-viral compounds. I teach Synthesis of Drug in the Faculty of Pharmacy.

Some of my research has been moving towards computational organic chemistry, and I being a theoretical chemist, will use this marvin to better communicate with organic chemists and to perform tasks like conformers search.

We develop libraries of materials for various biomedical applications ranging from gene delivery to stem cell differentiation. Currently, we have no structure depository for all of the compounds prepared (nor a common location for results). I am hoping to start using your tools to implement this.

I am looking for a tool to draw molecules and to predict some features

Investigation of molecular interaction from ab initio level to molecular mechanics.

Students use software to learn about naming and molecular geometry.

synthesis reactions with aldehydes and amines

Computation of logP and psa values.

Use of the academic package is required for my course in Organic Chemistry

Research – preparation of chemical structures and IUPAC nomenclature in publications Teaching – preparation of teaching materials for undergraduate lab practicals

Calculating thermodynamic properties of compounds

Hit to lead Optimization using marvin Specially the LogP calculator

molecular modelling work for receptor complex

I am currently a student who\’s studying in a Laboratory techniques in biotechnologies. I discovered your software recently and find it very usefull as a more powerful and more convivial (and mac compatible) alternative to ChemSketch. The purpose we will have of the software is to provide us students, with an easy way to draw, create, calculate and evaluate chemical reactions and molecules.

use for reserach

for research

TEACHING: I plan to introduce students enrolled in our Bioinformatics Program to the ChemAxon suite of tools. RESEARCH: I plan to use ChemAxon tools in my academic research program, and encourage my research students to adopt and employ ChemAxon.

I am trying to find a way to cluster compounds found in HTS with moderate to high scores. I am hoping to fine a useful finger printing method that can reveal structural leads for inhibitors.

Data Mining Group Project – Based on the article – High-Throughput Ligand Screening via Preclustering and Evolved Neural Networks written by: David Hecht and Gary B. Fogel Project:

I am interested in using the property prediction software for calculating various properties (i.e. pKa, logP, etc.) of a library of compounds that I have recently synthesized. I will accompany any values obtained with the software with a note in the experimental section of the manuscript that your software was utilized. I am currently a postdoctoral associate in the laboratory of Professor Robert Langer, whose manuscripts are highly read and cited. I will use the license only during my time at MIT, and can include a reference to the software in all published manuscripts where the software was used.

examining a set of compounds and export to excel

•Computer representation of chemical structures and electronic exchange formats - Database management systems in chemistry. - Descriptors, pharmacophores, chemical space - Similarity, diversity, clustering: design and analyzes of chemical libraries. - SAR classification models (Decision trees, SVM, Networks of Neurons) and QSAR regression models (MLR, PLS). - Validation and applicability domains of QSAR models. - Docking. Virtual screening, hit selection. Lead optimization.

We investigate complex molecules of biological interest in super sonic jet.

Our lab searchs for molecular imaging probe and could use your software to analyse them.

Molecular characterization of Staphylococcus aureus enzymes. The study are focused on activity, pH optimum, thermostability, substrate specificity, inhibition by substrate analogues and metals of the enzymes.

I would like to learn your software suite for building 3d models of organometallic transition metal complexes. I am learning a lot of computational chemistry and I need a good software program to generate 3D coordinates for DFT input files. I found your software on the internet earlier today and it made me want to immediately stop using my chemDraw and chem3dDraw.

We are trying to build up an easily accessible database of our compounds and the JChem applet seemed to be the right tool.

Calculaing lengths and geometrical properties of synthesised molecules.

Will use as an alternative to ChemDraw: drawing chemical structures, reaction schemes, etc.

I would like to use the products in my research work focused on antimalarial compounds.

The research is devoted to in silico early drug discovery in the field of neuroidegenerative diseases (transmembrane receptors). This software will also be used for the educational purposes of in silico assisted drug design for graduate students. PS Please contact me by personal e mail, the department s contact can be rather slow, not answering or loose your emails.

teaching: for chemoinformatics educations in our department. reserch : for development chemoinformatics tools.

Interaction between ligand and protein

Currently the research is centered round the glucopeptide antibiotic vancomycin. By use of micro-cantilever arrays we try to both further the understanding of antibiotics and use several model systems to investigate mechano-chemical effects. These mechano-chemical interactions is what we detect using our cantilever arrays since the chemical reactions changes the surface stress on our cantilever arrays and hence can be used to determine binding constants etc. Charge plays a important role in our studies, so I appreciate the charge and pKa calculation packages.

Undergraduate students involved in drug discovery project of protein-protein interaction.

Undergraduate students involved in drug discovery project of protein-protein interaction.

I am developing a chemoinfomatics module for a medicinal database, for that i require Marvin

Undergraduate student involved in drug discovery project of protein-protein interaction.

Development of a database for myxobacterial natural products, consiting of a MySQL backend and a GUI frontend programmed using .NET technology.

We research about crystallization of pharmaceutical compounds. Many of compounds have complex structure. Thus I need your software to deskribe the compounds.

I am developing a graduate course in chemoinformatics at NCCU. We will be analyzing HTS data and performing structure based similarity searching and clustering.

I will use it in my lectures and practical courses about cheminformatics and modelling In research, we would like to use the program of OntoChem (Lutz Weber) which includes your software.

Our theoretical research is based upon nano electro-mechanical systems where we typically calculate the electronic properties using density functional codes linked to molecular dynamics. We find that to implement many of the calculations we need initial starting configurations which will be facilitated by using your suit of applications. If our group finds that your product is useful then we will look to make extensive use of it in the future.

We are working on structural bioinformatics projects and would use Chemaxon and its tools for analyzing small molecules and ligands.

Povide a tool for students in the virtual tutorials of organic Chemistry

I hope to find a program that will satisfy my needs. I plan to use the Instant JChem software to have an overwiev of the chemicals that I use in the lab.

Predicting Log P/D, smiles for metabolic products.

Use for teaching material for students

Used to teach others in learning labs and extended study classes to show different views and understanding of how molecules react.

Molecular modelling

I lead a research group focusing on biochemical and small molecular responses of plants to abiotic stress. We have established a metabolomics laboratory with the aim of analysing metabolites from various sources, including model plants and animals (e.g. blood, liver, muscle samples). We use mainly GC-MS, HPLC combined with UV-Vis, MSn (ion trap), electrochemical (Coularray), and charged aerosol detection (Corona). My teaching includes courses on metabolomics or small molecule analysis, at our University and also at the University of Helsinki. The software would be used mainly for research purposes, but I would like to introduce the software package and it functionalities to our students during metabolomic courses. I am not yet very familiar with all the possibilities that this package has, and thus, including all possible aspects of use is rather difficult. I would imagine that at least editing, manipulating and visualizing chemical structures, connecting the structures to their physicochemical properties, and converting between various chemical file types would be useful tools. We also do analyzes on the metabolic fate of xenobiotics, for which the Metabolizer may be useful. Currently we do not have good solutions for database related issues, but we have to look into it in the future.

I hope to find a software to manage huge databases. I have to search within these databases for possible metabolites that I found in metabolomic studies…

Doing research about chemical structure similarity. Need an API for graph matching and Fingerprint generation.

We are a drug discovery/structural biology lab. I have been looking for tools to help at the boundary between chemistry and biology.

Research: Data integration and molecular structure handling for metabolomics Teaching: Mass Spectrometry and chemometrics and cheminformatics at University of California, Davis

Parmaceutical Chemistry Research, Drugs Biotecnology. - Structure drawing - Results visualization - Virtual Library Screaning - Property calculation

Building of GPCRs focused library

Comparison of ligand-based and protein-based approaches.

At the course of Pharmaceutical chemistry to show pharmacy students an example of chemical compound database with its full functionality (ease of use under Excell interface, filtering and searching the structures).

complexation of the biology active compounds (NMR, UVVIS, MS)

Will be used to process a large chemical database (tautomers, protonation states) in preparation for use in virtual screens by docking against protein targets of interest.

Create visuals for lectures on second messenger sugnaling systems

Caclulation of pKa of a fluorescent chromophore from the priotein mTFP1

Should be used for showing the basics of chemoinformatics, for drawing structures, and for a chemical inventory.

structure biology

Use of the software for construction of complex chemical structures from simple starting materials in the most effective way.

To teach undergraduate student for example about pKa-values of different compounds and that different gropus in a molecule could have different pKa-values and the implementation thereof in analytical chemistry applications.

I use MarvinSketch to illustrate naming and conformations of organic molecules for Chemistry I and II and Organic I courses. The structures/names/conformations/charges appearing on my lecture-room computer screen are projected on a large view-screen for the students to see. I have not implemented the use of ChemAxon products on a website and I have no plans to do so in the near future. I do, however, advise my students to download MarvinSketch and use it to clear up ambiguities in names, conformations etc. for homework purposes.

Medicinal Chemistry and Bioorganic Chemistry purposes

I want to use the software for pre/post-processing before/after ligand docking.

Research for a PhD degree on Organic and Pharmaceutical Chemistry.

I am a student and I need a key License to enter certain plugins for my homework using my academic package for ACE ORGANIC.

Drug discovery.

This software will be tested for use in a Computational Chemistry course with focus on organic and pharmaceutical chemistry.

I just want to know how this marvin skecth will be useful for our project to draw chemical strutures.

Since I work with microchip electrophoresis it is very useful to be able to calculate the charge of various molecules at various pH. Our goal is to separate amyloid beta peptides for Alzheimer\’s diagnosis. Now I have tried Marvin and found it very useful! Therefore I would also like to have a teaching license, to use it when I teach students, e.g. two students currently doing their bachelor project under my supervision.

Molecular modelling of alternative substrates for an enzyme of interest and determination of possible conformations of alternative substrates.

QSAR studies of serine hydrolase inhibitors and ion channel blockers.

Current Undergraduate Researcher at UT Austin. Participating in individual research project in the Magnus group at the university. The aim of this group is natural product synthesis with interests in methodology. The software will be used to diagram reactions for presentations as well as create a digital database of my reactions. It will also be used to create images for a manuscript to be turned in to the university as well as any papers published.

Currently my work involves the geometry optimization of several natural products and the prediction of their in vivo activity based on thermodynamical parameters and distribution. We’re also studying some new antibiotics for some specific medicinal applications. All this requires huge amounts of molecules to be processed rapidly and choosing just a few to work on. The present approach (run all calculations for all molecules), albeit fast at the semi-empirical level, is, from my point of view, useless with the preliminary results I got using the online plugins at ChemAxon. The results I got with those plugins are essentially the same I got with the calculations (for example, in a list of 10 000 polyphenols, the “do it all” strategy selected about 250 compounds to go on, and the plugins got those 250 plus an extra one. On the side, I also do some computational work for other groups, typically people requiring fast results, and there I’d be thrilled to give them the Marvin immediate results and tell them “here they are, if you want the same results in the usual way just give me two or three weeks”.

Show how protonation changes logP of amino acids to students.

Screening large libraries for activity against several protein misfolding diseases. This program will be used to organize the data and guide SAR efforts.

I a intend to use this license to use the full form of Standardizer for processing large sdf files for computation of molecular descriptors for chemoinformatic analysis.

chemical descriptor calculation

For drug discovery and QSAR purposes

Teaches Graduate level introduction to biochemistry Chem641. Class has typically over 100 students per semester. Wishes to use the software to prepare class lectures and slides.

Our small lab is attempting to find a high affinity ligand for our protein of interest. this is our first foray into virtual screening of ligands and are trying various packages. We are most interested in the screenMD software program,as we are using other programs, particularly autodock vina, for the finding the initial ligands of interest, and are looking for programs for scaffold hopping.

I am using JChem to open Japanese ethical drug structures to the internet and to make groups by structural similarity in these drugs.

calculation of molecular descriptors (log P)

I will use the software to create chemical structures useful for my teaching course and to be inserted in my publications.

i am doing m.pharm pharmaceutical chemistry in srm college of pharmacy i required this software regarding project purpose regarding the properities of synthesised compound

For cheminformatics research..

We are studying experimental methods to measure logP and pKa or organic compounds and wanna use calculation as a comparison.

Macrocyclic nitrogen containing ring systems with a view to imaging. Use of software in internal report writing (if papers are published i wont write them, my boss will).

To calculate molecular properties of bioactive compounds

For personal use only. I\’m intrested in drugs and want to create my own, personal database.

Collection of individual researchers for neurotransmitter inhibitor research. Will be used in a core facility.

Using Combinatorial and Multi Component Reaction Chemistry (MCR). Creating virtual libraries of MCR chemistry and computational analysis of physiochemical properties of libraries.

Our lab is interested in the development and use of the tiny nematode worm Caenorhabditis elegans as a chemical-genetic model system. Our overall goal is to discover and characterize novel small molecule tools to probe the biology of animals. To find new bioactive molecules, we screen libraries of small organic compounds for interesting phenotypes in worms. We use both gentic and biochemical techniques for downstream target identification. We have used this approach to establish C. elegans as a powerful platform in drug discovery (see our Letter to Nature – PMID:16672971). Given that we screen large chemical libraries, and endeavour to continue screening new libraries, it is important that we have the tools to interpret, organize, manage, and manipulate chemical information. ChemAxon software provides these functionalities, particularly the JChem plugin for Excel. Your software will not only aid in our research, but will improve the experience of new graduate and undergraduate students in the lab. In the future, we would be happy to cite ChemAxon in all relevant publications.

We are profiling existing and novice human metabolites in our research. So, we are interested in predicting and exploring all the possible derivatives of a metabolite.

I\’m interested in identification of pharmaceutical metabolite in aqueous environment. For most pharmaceuticals and their biotransformation products, these pathways in the aquatic environmental are largely unknown therefore metabolizer software of chemazon will help for my reserch topic

I will use the software to create and display chemical structures in the Biology and Cell Biology courses that I teach (BSC 2010, and PCB 3023).

I would like to use for chemoinformatics research

Dear Sir, With best regard a brief description of my teaching & research is represented below. I work on Ab initio quantum mechanical methods together with DFT, TDDFT, MC and MD. My works hover around the determination of thermodynamic parameters like pKa, acidity, basicity, rate constant of proton transfer, determination of anharmonic frequencies and subequent impact on energy paramenters of chemical interest. I do have some research pubilications starting from modifying CNDO/2 and working out methods for determining the Solvation energy of molecules and ions in their singlet states apart from some papers on Graph theory and Group Theory. My works necessitate the geometry optimization (global minimum) and thereafter Hessian computations using VSCF methods. I am in touch with eminent scientists working in the same field at present. I teach Quantum Chemmistry and Spectroscopy in the Post Graduate classes in our sister concern (DCCS, Rahul Foundation) together with teaching Chemistry, Material Science and Environmental Science in the B. Tech Engineering Degree level classes. I would request for kindly issuing me a free academic license for JCHEM and MARVIN. I shall cite ChemAxon as per your prescription in all future publications in this regard. Since my teaching and research is purely academic and also absolutely non-commercial, I pray for kindly giving me free license for the evaluation of the afresaid softwares and my future contribution to the forum if kindly accepted me as a forum member. Looking forward to your kind consideration. With best regard, Dr. Biren Hazra, Assistant Professor of Chemistry, Department of Applied Sciences, Durgapur Institute of Advanced Technology and Management, G. T. Road, Rajbandh, Durgapur, West Bengal, India. PIN 713212

It will be used for writing a structures and reactions for a papers. It will be use in my project \”Synthesis of a novel organometalic antiestrogenes\” for a calctulation of some properties of a compounds.

Making chemical database

For Structure

Draw structures on Linux

I’m using Marvin Beans for educational purposes in school, like visualization of molecules in 2D/3D in class. Furthermore I’m using it to create molecules for handouts, tests, etc. while preparing for the next lessons.

Our research aims are to examine drug targets and their interactions with ligands using modeling techniques (homology modeling, molecular dynamics simulation, docking, pharmacophores).

Current research consists of investigation of the structural and funictional role of key non-active site residues that may be involved in P450 2B4 plasticity through residue-residue interactions, hydrogen/deuterium exchange-mass spectrometry of P450 2B4 in the absence and presence of 4-(4-chlorophenyl)imidazole, 1-biphenyl-4-methyl-1H-imidazole, and ticlopidine, and efforts to crystallyze P450 2B1, 2B4, 2B5, and 2B11 with a set of small molecule mechanism based inactivators. The research will involve elucidating product profiles from a set of mutants of P450 2B4. The research will require represenatations of small molecules, and prediction of mass spectrometry data for the LC-MS analysis of products would be helpful in experimental design and analysis.

Glycobiology: Interactions of carbohydrates with proteins, e.g. sialic acids with Siglecs

For teaching drug design by computing and large scale virtual screening.

learning tool

Study structure-activity relationship in high throughput screening experiment.

Presentation of chemical structures and structure function analysis the course: Pharmacodynamics and Applied Therapeutics SAR analysis of newly synthesized and target screened compounds

The provided software will be used to teach organic/medicinal chemistry courses to the undergraduate students in chemistry of our College.

I am working as a Associate Lecturer for Bioiformatics at KIIT School of Biotechnology,KIIT University.Simelteneously i am also doing my PHD work in Computational Drug Designing for Anti Malaria Drug Development. For teaching in Bioinformatics specifically practicals in connectection to Computer Aided Drug Designing and also in view of my PHD research work i need the Marvin Software with a academic license.

Building chemical structure database for QSPR analysis

Study of ligand pKa values.

Research Aims I am specifically interested in using MolConvert to work on in silico screening of ligands for in silico marine toxicology studies. Teaching Implementation I am co-teaching a course on evolution, including molecular and protein evolution, and am developing a course on bioinformatics and molecular evolution tools. Software demonstrations will be a part of the second course.

To enable students to draw and visualize organic molecules in synthesis.

I am a postgraduate student in Guangzhou university . My major is Organic Chemistry. In school of Chemistry and Chemical Engineering

The Burton research group is primarily interested in OrganoMetallic characterizations.

I am going to use tools for teaching chemistry in the classroom.

Teaching school children of the 3d structure of molecules

Preparation of presentation materials.

Research areas are computer-aided drug design and medicinal chemistry. Specific topics include FAAH and MGL inhibitors, CYP-active compounds, nuclear receptor ligands and GPR55 ligands.

chemsketch to draw and then cxcalc use to calculate descriptors of various chemical entities for further data mining

My professor, Dr. Kevin Jantzi, is looking for an alternate program (instead of Win-PLT) to use to create homework assignments and exams for his students. He is professor of organic chemistry at Valparaiso University. His email address is kevin.jantzi@valpo.edu.

Comparative analysis of positive hits in drug screening for undergraduate research project.

Necesitamos comparar un par de moléculas y mostrar la parte diferente de una respecto a la otra.

Will be used to provide descriptors for monomers and cationic polymers such as length, pka, hydrophilicity, rigidity and other parameters that will be used for quantitative structure activity relationships

Molecular modelling. File interconvertion. Generation of virtual compounds.

Lignad and structure based drug discovery

Project related to protein protein interactions

Teaching: molecular visualization and modeling Research: design of ligands for virtual screening

Dr. Bearss is involved in researching small molecule drug activity, the use of genetic model systems in drug development, and translational research focused on identification and validation of new targets for cancer drug development. We have a research group that includes students and post-doctoral fellows that are learning to use computational tools for structure-based drug design and SAR model development. We are are interested in using Chem-Axon tools in training of these students and post-docs as well as implementing their use in the research conducted in the lab.

I am using this software to help me while I am attending school at the university and taking classes in chemistry.

We will use these programs to draw and evaluate the chemical and physical properties of several organic molecules known to binding to a multispecific drug binding protein.

Preparing images of ampipathic sturtures used in screening experiments

treatment of pharmaceuticals and personal care products

The software will be used to aid metabolic reconstruction projects for several halophilic archaea. In particular, plugins associated with theoretical calculation of factors affecting reaction thermodynamics (e.g., protonation states) will be used.

The tool will be used for developing a marine compound database , for teaching purpose only

Perform structure search, drawing, visualization, and learn how to use diverse tools for further implementation of own scripts.

Functional genomics, review compounds structure then to reactions and pathways

I will try to use this software in teaching of General and Inorganic Chemistry.

The database will be used for organic chemistry instruction. After making topic selections and searching to see if the entry had been taken by another student, students will add the molecular structure that is the topic of their project to the database. This will expose students to the use of a local database and will provide a mechanism for us to catalog entries.

The research is related to developing new methods for computer-aided drug design. ChemAxon software will be used primarily for analyzing chemical libraries and visualizing molecules.

Im a pharmacy student using this software for class.

I would like to try your softwares for the problem of lead optimization

Searching and classifying chemical databases, drawing chemical structures. Antibiotic research.

We want to make a library of drug like molecules and study their SAR. ChemAxon would be a great tool to compare the compounds.

Software used to calculate the compatability of polymeric materials with therapeutic drugs

I teach a class in molecular bioengineering and I want my students to be able to make property calculations on molecules so they can have a better understanding how structure relates to properties. Research will involve predicting transport properties of topically applied compounds for the prevention of HIV infection in the developing world.

* Use of Marvin applications to visualise and analyse protein-ligand complexes. * Use of InstantJChem to build local databases for virtual screening benchmarking.

Computational study of catalytic reactions that requires the partial charges evaluation and other important structural properties.

This software will be used for preparation of lectures presentations, research articles, Bachelor\’s and Master\’s Thesis

The software will be used by this instructor in teaching the following classes: 1. General, Organic and Biochemistry 2. College Chemistry 3. Organic Chemistry

Explore chemical structures for organic chemistry course.

we are leaning organic chemistry and i need a license for steriosisomers

I want to use this software to research molecular surface area.

CONDUCTING SUPPLEMENTAL INSTRUCTION SESSIONS AT LSU

Working on a total synthesis and need a drawing program that doesn\’t cost $1000. Would like to be able to calculate pKa values of intermediates synthesized during synthetic route to teach undergraduate chemists the importance of acidity values. Your software would greatly help.

I will be utilizing this software in the illustration of mechanisms that are involved in the formation of enzyme substrate complexes and their related bio-organic reactions.

In my courses I need to draw complex molecules and your software is really great for that. It really helps me in my work.

Want to try it first but plan to use the batch tools to plot structures of substances which are outputed in my network-topological analysis of the organic chemistry network.

I am a student at CSU Chico and would like access to this program so that I might utilize it to further my understanding in Chemistry.

I am currently teaching an online organic chemistry class that uses the ACE Organic platform and would like to use marvinspace to show details about stereochemistry.

ligand library construction and visualisation property prediction for early ADME tox consideration presentations/communication may be applied to teaching (master level) if satisfactory

Marvinbeans will be used towards and by upper secondary pupils learning chemistry. Specifically it will be used to view molecules in 3D, naming of molecules, identify isomers and simple reaction mechanisms. In addition pupils will use Marvin to solve assignments.

The applications of interest are for Organic Chemistry II. Molecular manipulations and other other forms of analysis are imperative when carrying out labs.

Research in Drug Designing Molecular modeling Theoretical Chemistry, QSAR Studies, Computer Aided Drug Designing

I wish using chemaxon soft for teaching chemistry in my high school

Maintaining and analysing a database of chemical compounds from the NCI for virtual screening against influenza and other targets. Use of the tools for postgraduate MSc teaching.

Pharmacophore mapping

Primarily the determination of speciation of chemical compounds at physiological pH

Computational drug designing and delivery system

teaching of inorganic and organic chemistry and biochemistry

Our lab is performing high-throughput screens to identify compounds that kill Mycobacterium tuberculosis. We would like to use the chemaxon software to help analyze our data (organize hits, etc). I am particularly interested in using this software in conjunction with Excel as a means to organize and edit structures.

We are designing transition state inhibitors of an enzyme, and my main aim is to do calculations of charge and geometry on candidate molecules.

DRAW STRUCTURES AND PROPRIETY CALCULATIONS

I am examining the transport of fluorescent dyes and other small molecules. I would like to use this software to determine the effective charge of these species at specified pH.

A the department of Clinical Pharmacology we look at the drug metabolizing enzymes Cytochrome P450s and UGTs.

Structural Bioinformatics

- analysis of our inhouse dataset of biomolecular contacts - comparison of protein-protein and protein-small molecule contacts

We are interested in using Marvin Viewer and ChemSketch along with our in house de novo design programme and virtual high throughput screening programmes to identify potential new inhibitors of a number of targets including RNA polymerase, DNA gyrase, plasmodium falciparum DHODH and several ion channels and transporters including aquaporins.

Teaching introductory Organic Chemistry

I\’m a student at Nebraska Wesleyan University and I found your software very helpful in assisting with my homework, and I tutor some students in the chem courses here and I think your programs would be very helpful in assisting them.

We are offering a lab-course on Computer-aided Medicinal Chemistry (CAMC): the aim is to teach the students to use modern software packages (MOE, ChemAxon …) for typical cheminformatics tasks like chemical database searching, compound filtering, structure based drug design, QSAR modeling… This is part of the curriculum of Life Science Informatics at the http://www.b-it-center.de/ . Current time table: http://www.b-it-center.de/Wob/images/36707871.pdf

I actually want to use ChemAxon tools to do reaction mapping and standardize my reactions.

Virtual screening and assessment of drug-like qualities of molecules.

Chemical interference with signal transduction

For 3D conformation building, scaffold extracting (e.g. Murcko Scaffolds) and physical properties estimation (logP, mw etc.) in library compounds.

Investigating the active site of the protein DNA adenine methyltransferase using the Protein DataBase files that are available alongside compound libraries that we are currently studying.

The software will be used to generate different conformers of chemical compounds. Properties of the different conformers (mainly size/shape related descriptors) will be calculated and subsequently used for QSAR modeling of the ecotoxicity of different groups of chemicals.

We run a high-throughput screening resource Center for Rockefeller and Cornell, and we support and teach students to use high-throughput screening techniques in their projects. We would use this software for Xcel to exchange lists of compounds and associated data and to sort this data.

I am a teacher in Chemistry and Mathematics at an upper secondary school in Oslo, Norway. Parts of my teaching is in the International Baccalaureate (IB) Programme, which offers pre-unversity courses in various subjects. My aim is to use the software for preparing worksheets for my Chemistry students, for writing instructions for practical work, as well as for making viewgraphs to be shown during classes. Being able to quickly make drawings of chemical structures would greatly facilitate this work.

Research in synthetic chemistry Teaching at different levels and disciplines (molecular modeling – combinatorial chemistry – carbohydrate synthesis)

We do small-molecule screening, primarily for inhibitors of human transport proteins. In these projects we need to visualize ligand structures, analyze substructure fragments, predict pharmacophoric features etc.

to improve drug development

I am completing my final year undergraduate project and require the use of a Mac drawing program.

- visualization of biological molecules - interaction of biological molecules with potential biologically active compounds - Drawing of new compounds with potential biological activity

I am developing very first public chemoinformatics database in New Zealand named as MolSeek. This is part of activity to create a basic infrastructure for drug discovery related research in an open environment. ChemAxon Toolkit will be used to support database queries, and to implement the filters so that scientist can download the a set of chemical molecules for docking studies.

Preparing schemes.

I will use the program to help me with Organic Chemistry class

Inhibitors design for Granzyme B

I am student who is currently applying for research and would like to use such tools to enable easy navigation through a chemical database

My research activities include similarity search of ligands from publicly available small molecule databases and to find out whether similar molecules bind same targets . In this connection i am planning to use chemoinformatic tools from CHEMAXON for assessing the structural and substuructral similarities between small molecules ligands, chemical calculations, structure activitty relationship(QASR) etc. Apart from the invaluable use of your resources for my research actvities, it also will be used for teaching and practical demonstration of chemoinformatic tools for juniors and other interested colleagues(as we are having drug design and chemifomatics subject in our course).

Mainly Marvin Sketch to model chromophore structures for Gaussian/Gamess calculations. The conformer search function is quite useful and the work flow of Marvin is nicer then GausView.

Parkinsons research

Search and retrival of vendor libraries and create organize the 2D structures files. Use these structures for screening and if found any interesting structures, publish the work. We will cite the Chemaxon useage in all our publications.

Used for teach mechanism of reaction in Heterocyclic Chemistry to chemistry student

The software is being used in our metabolomics research as a way to organize and search through metabolite databases.

Our overarching research interests are in finding chemical reagents for use in biology. We use virtual screening as a main source of this and also work alongside crystallographers developing fragment based approaches to ligand discovery. Key to this is the creation of suitable virtual libraries. We wish to use chemaxon property calculators to characterise our libraries. Access to these products will help support the education of post graduate students through their understanding of virtual library construction and characterisation.

Currently developing mass spectrometry methods for a variety of compounds and will use to calculate pKa to aid extraction processes and visuulise mass fragmentation patterns

i’m working on calculations (quantum chemistry) and experimentations (solid-state nmr) of nmr properties of large systems (peptides, proteins) to determine their orientation and dynamics inside membranes

I intend to set up an inhouse small molecule database for high troughput screening and compound library generation. I want to test chemaxon’s fingerprints,pharmacophore and fragment detections packages to see if they are fit to this project.

Screening of molecules DBs using pharmaocophore templates to identify candidate H4 inhibitors

I work with the molecular pharmacology aspect of GPCR activation mechanism and will use the ChemAxon programs to calculate physical properties and visualize ligands that I work with.

Research aims include elucidation of synthetic organic pathways for the asymmetric synthesis of alpha,alpha-disubstituted amino acid derivatives.

In-silico design of new molecules active against different biological targets.

I will use Marvin primarily in my Advanced Inorganic Chemistry course, as well as my Advanced Physical Chemistry course. Marvin will be used to quickly and cleanly generate structures that can be imported into the program Avogadro.

Use in conjunction with other mathematical computational methods in prediction of products of complex organic synthesis mechanisms.

We would like to use the provided tools mainly for teaching in courses for MSc students in computer science and applied mathematics.

chimiotheque

biochemistry 740/745, drug design drawing molecules for use in sybyl

Generation and analysis of large molecular databases

we are doing a qsar study on the project in cox1 and cox2 inhibition activity is studied and compared

I’m research about new antimicrobial peptidomimetics active against bateria that produce biofilms

QSRR, Bioinformatics, Protemics

The aim of using Marvin program is to provide pKa and LogP estimation for chemical compounds. These estimation will be used to predict the coefficients of partition between tissues and plasma for the compounds studied (using QSAR models)

cadd, structure comparison

Search smiles for molecules

The software is currently used in a high school environment for drawing structures for lessons and handouts, and studying molecular architecture and nomenclature. I would like to extend this to some of the other functions, e.g. isoelectric point.

I am working in the chemoinformatic area and I need to use some chemaxon tools for my research.

Biomedical and chemistry studies.

I will be using the package to aid me writing my thesis.

To determine the microprotonation states of heteroatoms in scaffolds and the macroscopic charges of the scaffolds before enumarating virtual combinatorial library.

Inventory of teaching lab chemicals. Organic structure drawing and analysis for sophmore organic chemistry.

This will be used for teaching and research with some fellow students at UCSD.

I plan to use the software in aspects of structure activity relationship of compounds tested for activity in alzheimers disease and cancer.

Physical chemistry properties of various drugs

chemical genomics

would like to be able to utilize drawing program for Pre-AP and AP students: 1) to be able to show them structures pertinent to their understanding and 2) to allow them to be able to draw structures in order to help process their understanding

Utilised for my masters degree. Studying organometalic drugs in vitro. I’d like to add a chemoinformatic component to my thesis to compliment the labwork.

My research concerns with developing new paradigms of molecular modeling for predictions of thermodynamic properties of complex mixtures. I’m mostly interested in the Java API to bind the functionality of the implemented packages in the framework of molecular design and structure-property relationships.

We will be using the product to draw structures, look up structures and use the metabolize to find the metabolic pathways of naturally occurring products.

We are working on computational drug design using various tolls

I am a student In PSE department in Umass Amherst and my research deals with synthesis of small molecules for testing anti-bacterial activity against gram-negative bacteria. I need this software to evaluate the effect of conformation, polarity and other related properties on the activity of compounds

working on biosensor for the detection of influenza A

master thesis in toxicology prediction of acute toxic effects

Entirely for research based work based on protein-ligand interactions.

Maintaining compound libraries & management.

Development of automated QSAR workflows

I am a Marvin user and have registered on Marvin web. I have used Marvin Instruments several years. Zeta Nanosizer, Laser 2000… And I cited them in my papers several times. I mainly interested in the interficial molecular biotechnology, including molecule dissociation (pKa), Molecule charges, Protein Isoelectropoint, polarization characteristics… I hope to get the licence of ChemAxon. So I can get the fully use of the software and cite it. Thanks.

Drawing of chemical structures for conference presentations, determination of pKa values.

drug design, Molecular Modeling

I would like to use your software to generate conformations of small peptide derivatives to assist in interpreting changes in the FTIR spectra of the molecules when they are put under high pressures in solution.

FOR DRUG DESIGN

We do screening of chemical libaries looking for chemical probes of biological processes. These studies have resulted in > 15 publications since the beginning of our group. We are interested in using Instant JChem to help us to manage our chemical library and plan for new additions.

drug design prediction of physicochemical properties

Immobilization of molecules at the nano scale.The program will be needed mainly for structure drawing.

Organic Chemistry

Protein structure & docking

for teaching in Chemical and Life Science Department Undergraduate Students in Senior Design projects

I’m currently a graduate student working in the lab of Dr. Linda Broadbelt at Northwestern University. My project primarily involves the fields of computational chemistry and molecular modeling. My access to this software will be used to interpret the MDL molfiles output for our biochemical network generation software.

chemical structures

Dependence of biological activity on molecular structures and properties.

Teaching subjects on Organi and Computational Chemistry

about national products and their acitvity