To facilitate the creation of a central structure hub for databases such as DrugBank and the Human Metabolome Database at the University of Alberta, we have integrated JChem Base with Ruby on Rails, a robust web-application framework. By using JRuby to bridge the Java and Ruby world, we have built a scalable solution for storing, retrieving, and searching structures. This presentation will discuss the implementation details and advantages of building a simple, standard, and web-accessible structure hub.

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While many software systems exist for small molecule structure representation, drawing and registration and are widely used by biotech/pharmaceutical companies in small molecule drug discovery, there is no system available designed specifically for large molecules. This talk begins with a review of the challenges in large molecule structure representation and the shortcomings in using small molecule systems for large molecules. A notation language to represent large molecule structure will be presented, and examples will be provided on how to use it for modified oligonucleotides and peptides. A Graphic User Interface (GUI) tool will then be presented to demonstrate how to construct a complex large molecule structure, such as siRNA with chemical modifications. Finally, the talk will discuss a large molecule registration system, with focus on structure uniqueness checking, validation and verification.

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SkunkWerks used JChem to provide substructure and similarity searches across an existing Screening Library System. The solution was integrated with the existing RIA applications and SkunkWerks proprietary back end. SkunkWerks opted for JChem’s Web Services as the means to communicate with JChem Base. Using JChem’s Web Services SkunkWerks was able to seamlessly integrate substructure/similarity searches into the application. This session will present the solution that was developed using JChem and Flex (Adobe Flex) for a RIA implementation.

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Not all biotechnology companies are focused on small molecule drug discovery, nor do they need to manage millions of compounds. However, these companies do synthesize novel compounds and must track related data. For example, Ambrx, Inc.’s discovery platform is based on a fundamental advance in protein biosynthesis that enables the company to genetically engineer proteins with new amino acid building blocks beyond the common twenty. Ambrx has a small, active, chemistry group that wishes to register compounds, assign identifiers, track batches, and associate analytical data. The cost of most chemistry registration systems force chemistry groups like these to do without. Ambrx uses our open source LabSynch software to track, analyze, report and share its protein-based drug discovery samples and data. We will describe how we integrated Instant JChem Enterprise with LabSynch to enable Ambrx to associate chemistry structure, batch and analytical data with their other discovery data.

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Metabolomics is part of the modern life sciences tree including genomics, transcriptomics and proteomics. One of the major goals in metabolomics is to identify small molecules including lipids, organic acids, sugars and amino acid and to obtain spatial and temporal snapshots of metabolite concentrations from complex biological matrices. The results are used to obtain greater insight into plant and animal metabolism and to understand complex cellular processes. Cheminformatics approaches play a crucial role in metabolomics because properties of organic molecules can be modeled in-silico and are matched against experimentally obtained result from analytical techniques including liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS). The accuracy of such predictions including octanol water partition coefficients (logP), acid dissociation constants (pKa) and boiling points (bp) are important to reduce the search space from millions of possible structural isomers down to a low number of potential candidate structures. Besides that, cheminformatics software tools must be able to handle millions of structures and a multitude of structure formats and should provide simple-to-use graphical front ends for novice users and versatile command line parameters for experts. We used Marvin GUI components including ChemAxon MView, Standardizer and Reactor as well as the JAVA API components in a metabolomics environment to generate molecular structures and curate mass spectral databases. The use of such databases allows the measurement of more than 150 metabolites in a single sample, requiring only few micrograms of biological material. Using our high-throughput analytical techniques we are able to profile several thousand samples per year. In addition to that, we show how the Instant-JChem program with its integrated overlap search and Marvin tools can be used as a general purpose tool for structure handling. We show how physico-chemical property calculations obtained from Marvin are used to support the structure elucidation process in metabolomics.

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OCMiner is OntoChem’s chemistry aware semantic search engine. Based on UIMA, OCMiner allows to annotate and subsequently search various information sources with concepts from chemistry, biology and related disciplines. Chemical structure searching, including sub-structure and similarity searches using ChemAxon functionalities as well as ontology based concepts are added to a Lucene based free text searching.

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In the current climate, cost and effectiveness is vital for survival.  At Evotec we are seeking to improve our ability to manage chemical data, to share that data more effectively with our clients and to allow our scientists to work more efficiently through automation of data management.  The decision to buy software such as an ELN, or products such as Instant JChem help to provide the scientists with the basic tools to do their job.  By enhancing these through integration, extension and enhancement by our in-house software team we aim to allow them to do their job in a more efficient and (cost-)effective way.  This talk will discuss our decision process for choosing an ELN (to work with ChemAxon tools), our plans for Instant JChem and data sharing with clients.

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SureChem’s database of more than 9 million chemical structures is generated by extracting chemical names from full text patents and converting them to chemical structures using a suite of name-to-structure conversion tools. SureChem has performed an evaluation of ChemAxon’s newly developed name to structure toolkit, comparing the results to those obtained by the other tools in SureChem’s current production pipeline. Results of that comparison and suggestions for future developments will be discussed.

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An Open Source initiative known as the Pistoia Partnership has been established to streamline non-competitive elements of the pharmaceutical drug discovery workflow by the specification of common business terms, relationships and processes. Initial focus has been on chemistry, biological screening and sample logistics.

Every pharma company & software vendor is challenged by the technical interconversion, collation and interpretation of drug/agrochemical discovery data, and as such, there is a vast amount of duplication, conversion and testing that could be reduced if a common foundation of data standards, ontologies and web-services could be established within a nonproprietary and non-competitive framework. Such would allow interoperability between a traditionally diverse set of technologies to benefit the healthcare sector.

Through global collaboration, this pragmatic community will derive, instantiate and make available web-services for consumption by Academic institutions, Vendors and Companies under an Open Source framework.

We will describe current progress, learnings and how companies, academics and others can participate in this approach.

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At Evotec we have been developing software using ChemAxon tools for more than five years. This talk will provide an insight into some of the applications that we have been building over the past year – including a new Web 2.0 Compound Ordering system connected to our own compound supplier database and the Symyx ACD and our ERP system, enhancements to our registration system that we introduced last year including handling tautomers, overlap searching and export preferences using the JChem cartridge.

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In response to increasing demand for software as a service and hosted cheminformatics solutions, DeltaSoft and ChemAxon have teamed up to provide a suite of fully hosted applications, including compound registration, inventory, bioassay, and structure activity searching and reporting.  The hosted solutions free IT groups from the installation, ongoing maintenance and upgrades of hardware and software infrastructure.  Users can access applications and data anywhere from a web browser.  The details of this approach and various implementation options will be discussed in this presentation.

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Using different hardware platforms / operating systems we have explored different possibilities to build and implement JChem based chemical-biological databases with more than 100 million chemical compounds. These datasets are then subject to various 2D and 3D similarity searching methods to provide ideas for novel molecules of biological interest. We will show examples for using these integrated technologies for lead finding.

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IBEX is a global AstraZeneca application to access GVKBio’s Medicinal Chemistry and Target Databases containing SAR data extracted from medicinal chemistry journals and patents. At GVKBio expert curators populate these databases with explicit relationships between published documents, compounds, assay results and sequences. A web-based application, IBEX provides an intuitive search interface to query more than 3 million entries representing over 2 million unique structures and 10 million SAR points. It uses ORACLE database technology and JChemBase and Marvin to handle chemical searches and structural visualisation. IBEX is currently used in medicinal chemistry projects for prior art checking, library design, ligand- and structure-based virtual screening. It allows AstraZeneca scientists (medicinal chemists, computational chemists, bioinformaticians) to explore wider relationships between ligands and target families. Examples of patent visualisation using, for example, ChemGPS chemical space and patent series identification using molecular frameworks will be given.

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The identification of promising chemical series from high through-put screening (HTS) data is an integral part of a therapeutic project, one which ultimately can determine whether the project will be successful. Despite its importance in deciding how to invest resources during the discovery process, analyzing HTS data is often performed in an ad-hoc manner using various combination of commercial and in-house tools. Furthermore, with the proliferation of available HTS data in the public domain (e.g., PubChem), the need for a widely available, easy-to-use tool to analyze and visualize HTS data has never been greater. To this end, we describe NCGC’s on-going effort to develop an open cheminformatics platform to address this need. The current platform embodies our collective experience in analyzing and visualizing HTS data across a large number of assays (>200) over the years. The JChem library, known for its maturity and robustness, has been instrumental in allowing us to develop a fairly feature-complete prototype within a short period of time. In this talk, we highlight some key features (e.g., standardization, data visualization, fragment-based automated analysis) of the platform and discuss its future directions.

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Using different hardware platforms / operating systems we have explored different possibilities to build and implement JChem based chemical-biological databases with more than 100 million chemical compounds. These datasets are then subject to various 2D and 3D similarity searching methods to provide ideas for novel molecules of biological interest. We will show examples for using these integrated technologies for lead finding.

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The Experimental Therapeutics Centre, the newest A*STAR Research Institute is located at the Biopolis, Singapore’s bio-medical research campus. ETC was formed to ‘mine the gap’ between basic and applied biomedical research, enhancing high potential projects in order to move them towards commercial development. To manage the various high through-put technology platforms that have been assembled at ETC in support of our mission, we have constructed an ‘Electronic Research Habitat’, a comprehensive hardware and software infrastructure designed to effectively manage terabyte dataflows in the context of ETC’s knowledge based workplace. We implemented ChemAxon as the Habitat’s cheminformatics platform and describe here our on-going development and integration of ChemAxon into our electronic environment.

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Palatin has implemented a robust cheminformatics solution based on DeltaSoft’s web applications and ChemAxon’s chemistry tools. Our ChemCart Registration, BioAssay, and Structure-Activity applications are powered by the JChem Cartridge chemistry engine and Marvin tools. With this implementation, researchers can update, search, browse, and share both chemical structures and related test result data (including files and images). This system allows for seamless communication across the scientific groups at Palatin, and will be described in detail during this talk.

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PubChem is the largest known public repository of biological and chemical data. One of the goals of PubChem is to archive and make the structure-bioactivity data available. The use of various data mining and machine learning tools such as SVMs, Decision Trees, Bayesian models, etc., or advanced searching tools like Markush, custom fingerprints, 2D and 3D similarity, is essential during the post-HTS analyses process. Intellectual property monitoring is another key aspect of PubChem data-mining. Thus, the process of extracting chemical and associated bioassay data from PubChem, processing, arching and storing it in an in-house compatible system is an important task, which can result in increased speed and processing ability, with respect to the above tasks. Once PubChem data is available off-line, data integration with existing in-house HTS or other bioactivity databases becomes an equally important task; the resulting integrated system would enable researchers to query, investigate and profile compounds in a much broader context. We used Instant JChem to create and populate a database containing the MLSMR library and associated bioactivity data from PubChem; further integration with WOMBAT was also performed. The resulting database can also be accessed using the standard JDBC interface with JChem API, and is also amenable to custom data mining tools or search algorithms. Lessons learned from PubChem data mining will be discussed.

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DockingServer (www.dockingserver.com) is an internet service developed by Virtua Drug Ltd that calculates the site, geometry and energy of small molecules interacting with proteins. It offers an easy and effective way for carrying out docking calculations, evaluating and presenting the results of docking calculations, writing method section for reports and organizes docking data.

DockingServer integrates the different tasks arising during the docking calculations by using third-party softwares for different steps. Molecular docking is based on Autodock software, electronic properties of the ligands are calculated with MOPAC and small molecule preparation and visualization are achieved using ChemAxon softwares.

The role of ChemAxon softwares in the DockingServer can be divided into three groups:
1. cxcalc calculations run in the background in order to i, calculate the protonation state of the ligands at a given pH; ii, to achieve rough geometry optimization of the ligands; iii, to calculate IUPAC names for the ligands;
2. file conversion tasks, like sdf conversion to multiple ligands, mol2 -> mol conversion etc. using molconvert command.
3. visualization and input of the ligands in 2D and 3D, visualization of the binding site-ligand interaction is achieved by using MarvinSketch and MarvinView.

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IBEX is a global AstraZeneca application to access GVKBio’s Medicinal Chemistry and Target Databases containing SAR data extracted from medicinal chemistry journals and patents. At GVKBio expert curators populate these databases with explicit relationships between published documents, compounds, assay results and sequences. A web-based application, IBEX provides an intuitive search interface to query more than 3 million entries representing over 2 million unique structures and 10 million SAR points. It uses ORACLE database technology and JChemBase and Marvin to handle chemical searches and structural visualisation. IBEX is currently used in medicinal chemistry projects for prior art checking, library design, ligand- and structure-based virtual screening. It allows AstraZeneca scientists (medicinal chemists, computational chemists, bioinformaticians) to explore wider relationships between ligands and target families. Examples of patent visualisation using, for example, ChemGPS chemical space and patent series identification using molecular frameworks will be given.

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Evotec have developed a Library Profiler tool based on ChemAxon toolkits to allow scientists to analyse and filter large combinatorial virtual libraries into smaller libraries or compound sets.

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Not only Computer Chemists but also various researchers access a lot of different software and data resources in a broad range area in drug discovery. The workflow solution that can deal with the combination of different applications and data sources as the protocol in the same platform is recognized as very effective tools.

“KNIME” is a workflow solution that Knime.org (www.kime.org) in Germany develops, and is distributed free of charge as open source. Major modeling software development companies such as SCHORODINGER and Tripos are already partners of KNIME. So it seems that KNIME considers the use of modeler as well as cheminformatician.

This time, Infocom released “JChemExtensions” that is able to use the ChemAxon tool with core capabilities for structure visualization, search
and management, property prediction on the KNIME. It also make use of the characteristics of chemical structure search engine of JChem, so
researchers can access chemical structures stored in a JChem data cartridge or other relational database on the KNIME workbench. We will demonstrate a number of nodes and show how easy it is to make.

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The Experimental Therapeutics Centre, the newest A*STAR Research Institute is located at the Biopolis, Singapore’s bio-medical research campus. ETC was formed to “mine the gap” between basic and applied biomedical research, enhancing high potential projects in order to move them towards commercial development. To manage the various high through-put technology platforms that have been assembled at ETC in support of our mission, we have constructed an “Electronic Research Habitat”, a comprehensive hardware and software infrastructure designed to effectively manage terabyte dataflows in the context of ETC’s knowledge based workplace. We implemented ChemAxon as the Habitat’s cheminformatics platform and describe here our on-going development and integration of ChemAxon into our electronic environment.

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Recently, the amount of the data, which medicinal chemists have to deal with, is rapidly increasing from HTS, CombiChem, and other high through-put technologies. Also it has become common to consider ADME and toxicity characteristics from the early stage of research, which diversify the data source and research team members. Therefore, in the medicinal chemistry research, we definitely need an environment which enables various members of the team to access the diversified data source efficiently.

In order to deal with the increasing data, Teijin Pharma have introduced and applied an assay-database, a compound-database, and other cheminformatics tools. Last year, in the view of maturity of information technologies and of generational change of compound database systems in these days, we changed the main compound database system from ISIS to JChem, and developed a new compound database system. We now started to integrate other systems to the compound database system.
In this presentation, I will describe the concept, plan, and implementation of the recent development of cheminformatics systems at Teijin Pharma.

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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. According to Laffort et al. (2005) the most accurate and not too complicate experimental method to establish these experimental parameters is probably the gas-liquid chromatographic experimentation (GLC) with five different stationary phases. However, because some solutes of very low volatility are difficult to study using GLC, 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. This later method is fully described by Laffort and Héricourt (2006).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 (δ5), orientation (ω5), polarizability-induction (ε5), acidity (α5) and basicity (β5).

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Within the framework of an ongoing, ANR (Agence Nationale de le Recherche) – funded project aimed at developing innovative flexible docking algorithms based on massively distributed GRID calculations, the web portail for the submission and analysis of docking runs by future Academic users is heavily relying on the ChemAxon toolkit, notably for the pre-docking treatment of the submitted potential ligands: 1.Standardized representation, including counterion detection/deletion (Standardizer) 2.Enumeration of microspecies and potential tautomeric forms according to a user-defined policy (dock major microspecies/tautomers, dock several microspecies/tautomers or dock compounds in protonation states as presented in the input file) 3.Fractional charge calculations for each microspecies/tautomer 4.Empirical force field typing for each microspecies/tautomer, using Pmapper with custom-made XML setup files 5.Generation of initial 3D structures as starting points for distributed conformational sampling and/or use of the ChemAxon conformer generator to provide a set of possible geometries for the unbound ligands 6.Storing of already built multiconformational sets of compounds, using JChem 7.2D/3D visualisation of individual ligands using mview and display of docking poses in mspace. The presentation will, after a brief discussion of the planned docking strategies and algorithms, make the point on the current progress on the seven above-mentioned aspects, highlighting the strengths and the wish list of improvements of involved ChemAxon tools.

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In this paper we shall discuss some of the drivers behind the increasing number of pharmaceutical and biotechnology companies moving from traditional proprietary chemical information systems into modern alternatives. We shall explore the business drivers for change and discuss some of the issues which must be considered before migrating chemical information, including an analysis of common issues. New approaches such as systems biology and translational medicine demand interoperability and integration of data and systems. Oracle data cartridge technology offers the opportunity to break the dependency between a pharmaceutical company’s data and the software that manages it, encouraging an increase in the utilisation and value of data. We shall discuss the benefits of this approach and explore how to achieve migration, focusing on the benefits of JChem Cartridge and the ChemAxon products.

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As a new structure search engine, ChemAxon’s Marvin/JChem have been evaluated and compared with MDL’s ISIS draw/ISIS host. We used 1.8 million compounds to create a testing database and 115 structures were evaluated including 51 simple sub-structure searches, 51 similarity searches, 64 complex searches, tautomers, double bond, stereochemistry, multiple substituents, valence, ring size, chain length, etc.

ChemAxon application provides more logical and chemically meaningful results in searches, and can perform bidentate and atom-type searches. In our evaluation, ChemAxon application showed better or equivalent search performance in general. On the other hands, MDL® can give unexpected results in similarity searches and provides various databases such as MDDR, ACD, REACCS, etc. The major differences between the two search engines result from aromatic bond definitions.

In terms of transparency, ISIS has proprietary data/table structure but ChemAxon gives clear understanding of flow of data, structure of data, execution process. Also, ChemAxon provides a simple SDFile processing and manipulation tools. In addition, ChemAxon provides various useful calculation tools including Elemental Analysis, pKa, logP, logD, etc.

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Drug-induced hepatotoxicity or liver damage/disease is a major concern during the drug development process. Toxicity knowledge exists but data is scattered in numerous sources and can not easily be accessed simultaneously. The goal of the Franco-Hungarian project KnowTox is to build a new knowledge base related to hepatotoxicity as well as predictive tools for the automated prediction of metabolites and their toxicity to extend the value of the system. Having access to a knowledge database containing detailed biological and chemical data and associated analysis applications will lead to better use of available knowledge and time and costs saving during drug development.

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When Biovitrum was spun out from Pharmacia Corp in 2001 we urgently needed a new system for storing biological and chemical data for the entire R&D organisation. It has become an efficient tool through which all data are readily available for analysis by all scientists and project teams. Structures and arbitrary assay data columns can be freely combined, and complex queries can be saved and shared between users.

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This presentation will demonstrate the wide variety of in-house developed applications that utilise Chemaxon tools at Evotec. The talk includes an overview of the Chemaxon tools we currently use, how we use them, how they are integrated into our applications, and what we plan to do in the future. The problems that have been encountered during this work and the associated solutions will be discussed. The presentation will conclude by focusing on our medicinal chemistry workbench application known as Esma, and demonstrate how useful drug design tools based on the JChem libraries can easily be delivered to the chemist’s desktop.

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Modern drug discovery relies heavily on large-scale high-throughput screening (HTS) to identify potential starting points for medicinal chemistry optimization. The typical “top X” activity cutoff method used to generate hits from large amount of raw HTS data is intrinsically error-prone due to the noisy nature of single-dose HTS, which oftentimes leads to a large number of false positives. Here we propose a novel knowledge-based, SAR-driven statistical approach for primary HTS hit generation using ChemAxon technology for clustering and chemical fingerprints. The method is also implemented with SciTegic Pipeline Pilot. In a proof-of-concept study for an in-house HTS campaign, the new approach proved to be more effective in identifying confirmed active compounds in diverse chemical scaffolds containing valuable SAR information, as demonstrated by a significantly improved confirmation rate compared to the traditional “top X” cutoff method.

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During the research process, scientists require easy access to specific data sources such as Chemistry data stored in a JChem data cartridge, various vertical applications including advanced chemical calculators and tools like the Marvin Drawing tool, as well as flexible and intuitive analytical and visualization tools. InforSense KDE with ChemSense leverages the power of ChemAxon to provide a powerful environment which makes the integration of data and tools easy. In order to give scientists the ability to address complex problems using pre-built or ‘build on the fly’ workflows that are reusable and flexible, we investigate the use of a number of ChemAxon components used in InforSense ChemSense. We will show how easy it is to construct meaningful workflows connecting ChemAxon functionality with other components relevant in the field of Cheminformaic research. Using a series of workflow examples, we highlight the use of ChemAxon tools to accomplish tasks such as creating vendor collections from SDF files, R-group decomposition as well as library design. Throughout these examples, the use of the ChemAxon JChem cartridge and Marvin tools make it possible for these tasks to be completed with ease.

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Among the knowledge databases developed at Aureus Pharma, AurSCOPE Kinase and AurSCOPE Ion Channels are focused on drugs described as kinase inhibitors or ion channel blockers, openers or activators. Both chemical and biological data are structured into a unique knowledge management system where chemical structures of ligands as well as precise description of their targets and biological activities have been collected from published articles and patents.
The present work is aimed to assess the chemical and biological diversity of both databases. A specific query was constructed to retrieve most active non-peptide ligands. 2D molecular descriptors were computed and their distributions analyzed. Afterward, to encode the chemical space for the whole active dataset (9897 and 8371 molecules for ion channels and kinases, respectively), ChemAxon’s chemical hashed fingerprints were generated and optimized. These fingerprints were then employed to cluster these datasets using Jarp algorithm as implemented in JKlustor module. Clusters and singletons distributions at different similarity thresholds were analyzed and linked to corresponding biological activity. The findings show how highly structured databases combined with ChemAxon solutions can be an efficient tool to assist and inspire medicinal chemists, biologists, and computational chemists involved in a drug discovery project.

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The recent application of chemoproteomics to rational drug design requires the development of information-rich databases enabling the cross-talk between the two worlds of Ligand and Target spaces. We herewith report several in-house generated datasets which could foster an integrated chemoproteomic approach to ligand design (i) a library of 1.8 million commercially available drug-like compounds (‘Bioinfo’) already set-up for in silico screening, (ii) a library of 21,400 non-redundant molecular scaffolds (‘SBI’) generated from the Bioinfo Library, (iii) a collection of 6450 druggable active sites (’sc-PDB’) from the Protein DataBank, (iv) a chemoproteomic database applied to human G Protein coupled receptors (‘hGPCR-Lig’) relying on precise information about 369 human GPCRs and 17,000 GPCR ligands, allowing to prioritize either scaffolds/ligands for user-defined receptors/subfamilies and vice-versa.

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The “click chemistry” philosophy proposed by Sharpless et al. can be succinctly described as synthetic route construction with an emphasis on the use of “easy” reactions, i.e. those with predictably high, context-independent exergonicities. What the quantitative statistical differences between the set of molecules accessible via click synthetic routes, and other relevant subsets of synthetically accessible molecules are, remains an open question. We are using ChemAxon’s tools to generate a virtual library of molecules that can be constructed using only click reactions in a small number of synthetic steps. By constraining our starting material pool to high production volume chemicals and using only click reactions, we hope to generate a virtually exhaustive set of “cheap and easy” molecules. The aim is to use the library to predict the distributions of properties and medicinal activities from molecules that should be “process” ready. Practical details about our methods for reaction specification and running ChemAxon’s tools on a parallel cluster will also be described.

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This presentation will demonstrate the wide variety of in-house developed applications that utilise Chemaxon tools at Evotec. The talk includes an overview of the Chemaxon tools we currently use, how we use them, how they are integrated into our applications, and what we plan to do in the future. The problems that have been encountered during this work and the associated solutions will be discussed. The presentation will conclude by focusing on our medicinal chemistry workbench application known as Esma, and demonstrate how useful drug design tools based on the JChem libraries can easily be delivered to the chemist’s desktop.

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Biotech industry must track chemical structure information throughout the scientific discovery processes. Packaged solutions are usually too expensive for smaller companies and provide more functionality than they need. Marvin Tools provide enough functionality to build a compact and efficient database system. In NeoGenesis, a biotech company recently acquired by Schering-Plough for its unique technology based on affinity selection, we have developed a complete system for storing and retrieving Chemical Structures and properties accurately with fine grained access levels. We used Marvin in Oracle to ensure uniqueness and to calculate molecular properties. The GUIs developed to interact with the system relied on Marvin Components. Marvin tools have saved us at least one year of development time and freed two employees to work on other applications.

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CTI’s Scientific Systems group was challenged with the task of building cost-effective cheminformatics applications that can be easily deployed to a world-wide enterprise. We have met this challenge with a data warehousing architecture and open-source-based Java development infrastructure, with targeted use of commercial tools and libraries. ChemAxon’s JChem and Marvin Java libraries provide core functionality for the molecular structure component of the data warehouse, the Java middle tier, and a browser-hosted user interface. This presentation will demonstrate web applications that use the Marvin sketcher for a web-based structure search, integrate JChem structure search results into a large and complex data model, and perform server-side rendering of structure images. In addition we will describe a mechanism for automated import to JChem’s structure tables from an MDL-based chemical registration system.

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The informatics team at the Genomics Institute of the Novartis Research Foundation (GNF) has been developing a comprehensive lead discovery database (LDDB) in order to support an aggressive drug discovery portfolio. The chemical structure searching capability of LDDB has been supported by the combination of Marvin and Daylight cartridge until 2004. However, we are migrating into an exclusive ChemAxon platform. This presentation intends to share with the user group our experience in using different vendor products, while focusing on the issues related to our cartridge migration process. Examples illustrating how ChemAxon tools are used in LDDB are also presented.

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InforSense Ltd, the leading provider of Open Discovery Workflow(TM) informatics platforms, integrates ChemAxon’s powerful and versatile technology within its ChemScience suite. Industry-standard Java components such as Marvin, JChemBase, Standardizer, Screen, Reactor, and Marvin Plugins (pKa, LogP, LogD) are seamlessly accessed via InforSense integrative analytic workflows and can link to different data sources and other products within the InforSense portfolio without programming. Capability highlights include multiple format conversion, handling and validation, a descriptor and fingerprint generation engine, a smart library design module, browsing and search capabilities, including sketch and search in deployed applications via the Discovery Portal. Close integration with InforSense bioinformatics and literature mining capabilities produces efficient informatics solutions able to handle complex research issues, previously very time-consuming.Sophisticated cheminformatics solutions combining different data sources, legacy or proprietary applications, external tools and web services are effortlessly built and deployed company-wide as reusable best practice solutions. InforSense’s visual programming environment and its Portal provide the framework for a single unified cheminformatics infrastructure. Indeed, multidisciplinary teams can now have seamless access to highly sophisticated and tailored solutions through the portal.

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Virtual screening and high-throughput screening are two major components of lead discovery within the pharmaceutical industry. There is an ongoing effort to deploy massive in silico screening (e.g. docking) on a GRID infrastructure using large libraries of compounds. The challenge posed to the medicinal and computational chemist is how to sift through the potentially large number of hits that can be generated by a (virtual) high-throughput screen in order to select interesting compounds for further follow-up. Hence, there is an increasing need for interpretation of large amounts of “noisy” data. Fortunately, the number of success stories showing that virtual screening helps in accelerating the rational drug design process is growing rapidly. There still remain significant challenges in the application of those approaches. Diverse tools running on different platforms having other data formats have to be integrated. The resulting large log-files with millions of entries have to be compared, sorted, merged and filtered before the results can be further analyzed by the project scientist.

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CTI’s Scientific Systems group was challenged with the task of building cost-effective cheminformatics applications that can be easily deployed to a world-wide enterprise. We have met this challenge with a data warehousing architecture and open-source-based Java development infrastructure, with targeted use of commercial tools and libraries. ChemAxon’s JChem and Marvin Java libraries provide core functionality for the molecular structure component of the data warehouse, the Java middle tier, and a browser-hosted user interface. This presentation will demonstrate web applications that use the Marvin sketcher for a web-based structure search, integrate JChem structure search results into a large and complex data model, and perform server-side rendering of structure images. In addition we will describe a mechanism for automated import to JChem’s structure tables from an MDL-based chemical registration system.

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We shall describe Kelaroo’s Reagent Management System (KRMS) that encompasses in-house containers and commercially available reagents (catalogue items). Functionality includes container and catalogue item searching, container registration, inventory tracking, reagent request generation and processing, requisition generation and integration with in-house purchasing systems, and catalogue item data uploading. The KRMS utilizes Marvin and the JChem Oracle data cartridge, and is designed to work in concert with Kelaroo’s Enumeration solution.

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We have begun the second phase of our research program intended to create a virtual classroom for teaching cheminformatics. This web-based project integrates concept-teaching with real-world software applications. Several vendors, including ChemAxon are participating by providing software, which will be incorporated into the e-learning modules. I will describe the overall goals of the project and demonstrate our first preliminary module. This module demonstrates the use of MarvinEdit for structure input, fingerprinting and ChemTattoo® from Mesa Analytics & Computing, LLC, OEChem from OpenEye Scientific Software, Inc. and MarvinView for color-coded display of results.

Our research results are based upon work supported by the National Science Foundation Small Business Innovation Research (SBIR) Program under Grant No. 0450457. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

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