Post subject: Migrating chemical information to new architectures
Posted: Thu Jun 21, 2007 1:23 pm
Title: Migrating chemical information to new architectures
Presenter: Andrew Lemon
Institution: The Edge Software Consultancy
Abstract: 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.
Post subject: Chemical Terms, a Language for Cheminformatics.
Posted: Thu Jun 21, 2007 1:28 pm
Title: Chemical Terms, a Language for Cheminformatics.
Presenter: Gyorgy Pirok
Institution: ChemAxon
Abstract: Flexibility and ease of use are important yet contradicting requirements in cheminformatics systems. Complex search criteria routinely used in database queries provide apparent examples. Beyond flexibility and ease of use efficient computability sets a third requirement.
To meet all these demands we have designed and developed Chemical Terms, a chemical computation language constituted of chemical functions (such as pKa, logP and many other chemical and structural calculations) and common mathematical and logical operators to combine these functions. The predefined set of functions can be extended using an open plug-in architecture.
Successful applications of the language including advanced search filters in chemical databases, virtual reaction design and pharmacophore perception are demonstrated. Future directions of the Chemical Terms language development will be discussed as well.
Abstract: Developments since the last UGM will be presented, with an open discussion of future plans. Main developments of the past year include table types, calculated columns, API improvements, reaction search improvements, new query atom types and Cartridge speed enhancements.
Post subject: Development of web-based compound database system at TEIJIN
Posted: Thu Jun 21, 2007 1:32 pm
Title: Development of a web-based compound database system at TEIJIN Pharma: Integration of the compound database and other existing systems
Presenter: Ryo Sogawa
Institution: Teijin Pharma Limited
Abstract: 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.
Post subject: Instant JChem - introducing the 2.0 alpha release
Posted: Thu Jun 21, 2007 1:33 pm
Title: Instant JChem - introducing the 2.0 alpha release
Presenter: Tim Dudgeon
Institution:ChemAxon
Abstract: Instant JChem is an end user application designed for biologists and chemists. It uses the Marvin and JChem APIs to provide powerful cheminformatics and data managment capabilities in a simple user interface. Version 2.0 brings some major functional improvements compared to 1.0, including multi-user access, the ability to handle relational data and a form builder, as well as various usability improvements. The architecture of 2.0 has been consideraby improved with view to providing APIs for extension by customers and third parties. A test version of IJC 2.0 is available for testing and the final version should be released shortly.
Abstract: Instant JChem (IJC) is a desktop application for scientists to manage information in local and remote databases. IJC should be thought of as an extensible framework for building rich chemistry and biology database-oriented applications. It is built on top of many proven and stable software components and libraries (NetBeans, Apache, Spring Framework ...) and adds chemical/biological specific software components. The core parts of IJC are Discovery Informatics Framework (DIF) and Instant JChem Core (IJCCore) modules. DIF brings a non-visual abstraction layer on top of relational databases and the JChem API. The IJCCore module provides the user interface framework on top of DIF. Through the APIs provided by these two modules, together with NetBeans, Marvin and JChem APIs, it is possible to plug a new modules into IJC. Lot's of IJC 2.0 functionality uses this approach and is implemented in independent plugins. There are several potential areas to extend IJC, such as adding new field types, new visualization widgets for the form designer, context sensitive actions to process data present in IJC, etc.
Post subject: An Integrated Approach to Library Design
Posted: Thu Jun 21, 2007 1:38 pm
Title: An Integrated Approach to Library Design
Presenter: Pat Walters
Institution: Vertex Pharmaceuticals
Abstract: A chemist designing a combinatorial library must consider many criteria when selecting reagents for synthesis. Factors such as target potency, physical properties, metabolic stability, and off-target activity are among many parameters that must be optimized. Although computational models exist to aid the chemist, these models are often poorly validated and are not easily integrated into the drug discovery process. As part of a continuing effort to provide library design tools for medicinal chemists, we have created a software tool known as Reaction Planner. This software provides an easy means of linking a virtual combinatorial library with a well-validated set of computational models. The application of these models can dramatically reduce the size of a virtual library, and help to focus a chemistry effort on the most relevant compounds. Models in Reaction Planner are constructed using NOMAD, an internally developed software platform that allows computational chemists to identify optimal combinations of molecular descriptors and machine learning methods. Models generated using NOMAD can then be published to Reaction Planner where they become part of the medicinal chemistry workflow. This presentation will provide an overview of NOMAD and Reaction Planner, as well as example applications
Abstract: Reactor is virtual synthesis engine able to predict products of given reactions and able to enumerate synthetically feasible combichem libraries. Beside a live demonstration of the core operations and introduction of the latest developments, we will give you an insight to our future plans with this continuously evolving tool
Post subject: ChemAxon's Marvin & JChem vs. MDL® ISIS/Draw ISIS/Host
Posted: Thu Jun 21, 2007 1:41 pm
Title: ChemAxon's Marvin & JChem (v 3.1.3) vs. MDL® ISIS/Draw ISIS/Host (v 4.0)
Presenter: David Roush (remote presentation)
Institution: FMC corp.
Abstract: 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.
Post subject: KNOWTOX, a Franco-Hungarian collaborative project relative t
Posted: Thu Jun 21, 2007 1:46 pm
Title: KNOWTOX, a Franco-Hungarian collaborative project relative to toxicity
Presenter: Elodie Dubus
Institution: Aureus Pharma
Abstract: 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.
Abstract: The latest ongoing development based on the Reactor engine targets the prediction of metabolic fate of drugs. You will see a preview of Metabolizer, a metabolic pathway and stability prediction tool, that is developed in the scope of collaborative project. With the help of a well designed metabolic biotransformation library, Metabolizer generates human phase I. xenobiotic metabolites. We will demonstrate the pre-alpha version of the tool and will explain how will the major metabolites and their stability be predicted.
Title: Integration of Chemaxon’s JChem with ChemInfoLogic software from Chemistry Logic
Presenter: Attila Berces
Institution: Chemistry Logic Kft., Hungary
Abstract: We demonstrate how we integrated Chemaxon’s JChem with ChemInfoLogic, which is a reconfigurable implementation of extremely fast chemical similarity searches and comparison of compound libraries. ChemInfoLogic complements current similarity search and library comparison software by making it possible to apply it to library sizes of virtual chemical spaces of hundred million compounds or more. ChemInfoLogic software is implemented on reconfigurable application specific computing technology and carries out key cheminformatics algorithms two orders of magnitude faster than CPU-based conventional software.
Post subject: DeltaSoft’s ChemCart: Next Generation Access to Research Da
Posted: Thu Jun 21, 2007 2:06 pm
Title: DeltaSoft’s ChemCart: Next Generation Access to Research Data
Author: Yvonne C. Shimshock
Institution: DeltaSoft
Abstract: ChemCart is a configurable forms interface to chemical structures / reactions, data, images, documents and files stored in a corporate repository. From a web browser that can utilize both Marvin and the JChem Oracle Data Cartridge as chemistry-handling components, scientists can query, browse, share, and update research information. We will describe how ChemCart can be used for Chemical Registration, Reagent & Sample Inventory, Electronic Lab Notebook, and Structure-Activity Relationship applications, as well as for rapid development of other R&D data interfaces.
Post subject: Jubilant ChemBioBase with LeadActiva? Powered by JChem
Posted: Thu Jun 21, 2007 2:36 pm
Title:Jubilant ChemBioBase with LeadActiva? Powered by JChem
Author: Dr. Sooriya Kumar.J
Institution: Jubilant Biosys Ltd. India
Abstract: Drug discovery scientists spend vast amount of time and money to scour meaningful data from the published literature. Given this, Jubilant has developed comprehensive set of target centric ligand databases that provide useful and important complimentary information on small molecules that exhibit activity against targets in a particular family. These small molecule databases integrate assay data and target information with chemical structures and the databases are built on the data captured from patents and scientific literature covering a wide chemical space of small molecules. The databases cover wide range of druggable targets from Kinases, Phosphodiesterases, Proteases, GPCR?s, Ion channels and Nuclear Hormone receptors. LeadActivaTM is the web-based browser interface for the Jubilant Small Molecule
databases powered with JChem Substructure search feature. The application is built on MVC (Model-View-Controller) by using Jakarta-Struts 1.1 framework along with J2EE technology. The back-end is Oracle9i. This presentation elucidates how Substructure analysis can be executed and QSAR datasets are retrieved from LeadActivaTM for better model building exercise.
Post subject: Integration of JChem in Kalabie Electronic Lab Notebook
Posted: Thu Jun 21, 2007 2:42 pm
Title: Integration of JChem in Kalabie Electronic Lab Notebook
Presenter: Ian Murrell
Institution: KLEE Group
Abstract:
Chemaxon and Klee recently announced a new offer integrating JCHEM. This lightening presentation highlights the key features of this solution now available to Chemaxon users.
Post subject: Development of a cyclodextrin database using Chemaxon tools
Posted: Thu Jun 21, 2007 2:58 pm
Title:Development of a cyclodextrin database using Chemaxon tools
Presenter: Eszter Hazai
Institution: VirtuaDrug
Abstract:Cyclodextrins are used as complexing agents in order to increase aqueous solubility of poorly soluble drugs in the pharmaceutical industry. Currently there are about 30 different pharmaceutical products on the market containing drug- cyclodextrin complexes. In order to meet the needs for a well-structured information source on cyclodextrins and their ligands, three Hungarian companies, Cyclolab, Delta and Virtua Drug have developed a cyclodextrin database using Chemaxon tools. Users can retrieve information from the database according to the structure of the molecule of interest, experimental details of cyclodextrin binding, calculated properties of the molecule and relevant literature. The database is for everyone involved in pharmaceutical industry, drug research, and researchers in the academic field interested in cyclodextrin complexation.
Post subject: Discrete Substructure Analysis at Merck Serono
Posted: Thu Jun 21, 2007 3:00 pm
Title: Speeding up the development of cheminformatics tools with Marvin, the example of Discrete Substructure Analysis at Merck Serono.
Presenter: Christophe Cleva
Institution: Merck Serono
Abstract: The development of new cheminformatics methods and tools can be very time consuming. We will show how the use of the Marvin library, and other 3rd party libraries (open-source or commercial), can alleviate and speed-up the development process. The example of the Discrete Substructure Analysis software suite at Merck Serono will be shown, as well as other tools developed by reusing the original components.
Post subject: Determination of solvation parameters using MarvinSketch
Posted: Thu Jun 21, 2007 3:02 pm
Title: Determination of solvation parameters using MarvinSketch
Presenter: Paul Laffort
Institution: Centre Européen des Sciences du Goût, Dijon, France
Abstract: 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).
Post subject: What's new in Marvin and development discussion
Posted: Thu Jun 21, 2007 3:03 pm
Title: What's new in Marvin and development discussion
Presenter: David Spender
Institution:ChemAxon
Abstract: The most important features and improvements in Marvin since the last UGM will be presented. We will introduce changes in structure representation and presentation quality graphics, show new plugins, file IO and plans for a new GUI design. We plan an interactive discussion about future developments of Marvin.
Abstract: IUPAC Naming is available in ChemAxon tools since April 2007. I will present the different ways to use it and evaluate the performance of the implementation.
Post subject: VERDI - An Extensible Cheminformatics System
Posted: Thu Jun 21, 2007 3:08 pm
Title: VERDI - An Extensible Cheminformatics System
Presenter: Patrick Walters
Institution: Vertex Pharmaceuticals
Abstract: As part of an informatics infrastructure which unites chemical and biological information, we have created VERDI - The Vertex Research Database Interface. VERDI is a cheminformatics system which provides an intuitive, user-friendly means of retrieving and analyzing chemical and biological data. The software employs a multi-tier client-server architecture which dramatically simplifies the integration of multiple databases with in-house and third party analysis components. This presentation will provide and overview of the VERDI architecture as well as examples of its use in drug discovery projects.
Abstract: Recent advances in maximum common substructure (MCS) based clustering is overviewed in this presentation. Special attention is paid to the accomplishment of the development roadmap presented at the User Group Meeting last year.
Abstract: The developments in the functionality of our Markush tools during the past year are presented and future directions will be discussed. Main developments include database integration, speed enhancements and Markush enumeration plugin for Marvin. Plans to extend the current prototype towards patents will be discussed
Title: Docking@Grid – A Web Portail for Massively Parallel Flexible Docking, using the ChemAxon Toolkit
Presenter: Dragos Horvath
Institution: CNRS
Abstract: 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.
Post subject: Introducing Parameter-Free Linear Relationship (PFLR) for 3D
Posted: Thu Jun 21, 2007 3:16 pm
Title: Introducing Parameter-Free Linear Relationship (PFLR) for 3D QSAR
Presenter: Ödön Farkas
Institution:ChemAxon
Abstract: The generalization of the DIIS interpolation scheme, used mostly in quantum chemistry, allows parameter-free prediction of molecular properties if a linear relation holds with the descriptors or scores.
The novel interpolation scheme was implemented for the purpose of QSAR predictions based on 3D descriptors. The automatic, common or pairwise, overlay of molecules is carried out using our pharmacophore-based procedure. Flexible molecules are currently treated via choosing the active conformers through building multiple models lead by selected conformers of the most active compounds.
Post subject: Integrating JChem, Marvin, and Calculator Plugins
Posted: Thu Jun 21, 2007 3:17 pm
Title: Integrating JChem, Marvin, and Calculator Plugins into a Collaborative Drug Discovery (CDD) Database for Neglected Diseases
Presenter: Barry Bunin
Institution: Collaborative Drug Discovery
Abstract: Collaborative Drug Discovery (CDD, Inc.) has developed a new type of collaborative web-database to help scientists more effectively develop new drug candidates for commercial and humanitarian markets. This technology allows researchers to build up networks of technical experts around therapeutic or target areas thus facilitating the discovery of new drug candidates. The initial focus was on neglected infectious disease; however the technology can be broadly applied to any therapeutic areas in academia or industry. The novel capability is the ability to archive data in both proprietary and open-access formats. The CDD technology focuses on collaborative drug discovery needs for distributed groups of researchers to archive and analyze chemical and biological data obtained from a range of both low-throughput and high-throughput screens including small molecule, enzyme, cell and animal bioactivity data. The CDD database uses automated data "mappers and slurpersTM" to automatically batch upload the assay data that researchers typically have in ExcelTM and sd file formats. This technology can provide gated access for private versus public groups at the individual experimental data level. The data can be "mined" at the molecular level, using keywords, chemical structure and advanced Boolean queries for multiple assays and their corresponding quantitative experimental values. The CDD technology has integrated ChemAxon tools to successfully build a platform for community-based drug discovery with an initial focus on infectious diseases of the developing world and global health.
Post subject: Corporate Registration System - A future solution
Posted: Thu Jun 21, 2007 3:19 pm
Title: Corporate Registration System - A future solution
Presenter: Akos Papp
Institution:ChemAxon
Abstract: ChemAxon started the development of a Corporate Registration System. In this presentation the required and planned features will be discussed, and the steps of the corresponding processes will be described. The design of the architecture of the system and the underlying database will also be presented.
Post subject: Instant JChem Direction development discussion
Posted: Fri Jun 22, 2007 6:43 pm
Title: Instant JChem Direction development discussion
Chaired by: Tim Dudgeon
Institution: ChemAxon
Abstract: We welcome feedback on the future development directions for Instant JChem. Current plans will be outlined and feedback from users and developers is requested.
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