Post subject: ChemAxon's toolkit integration into the Affectis Data MAn S
Posted: Fri Jun 22, 2007 12:13 pm
Title: ChemAxon's chemo-informatics toolkit integration into the Affectis Data Management System
Authors: Nkemdilim Uwaje and Markus Panhuysen
Institution: Affectis Pharmaceuticals
Abstract: We developed a Java-/PSQL based data management solution for our R&D. Sources of our data are as diverse as immunohistochemistry and in situ hybridization experiments, in vitro screening and EC50/ IC50 curves (plate reader), in vivo experiments, and last but not least small molecule structures and whole compound libraries.
Here, we present the architecture of our growing data management system and delineate the integration of JChemBase and the Marvin API.
Authors: Thibault Varin, Nicolas Saettel, Jonathan Villain, Aurélien Lesnard, François Dauphin, Ronan Bureau, Sylvain Rault
Institution: CERMN, UPRES EA 3915, 5 rue Vaubénard, 14032 Caen Cedex
Abstract: 5-HT4 receptors are implied in various peripheral and central functions, such as gastro-intestinal tonicity and secretions, as well as the modulation of emotional behaviour and cognitive mechanisms. Several years ago, our research center (CERMN) has launched a program for the discovery of new 5-HT ligands based on biological tests done in a screening center. This program led to new families of 5-HT4 ligands in the past years.1,2 The CERMN currently owns a chemolibrary of more than 10000 compounds including one thousand 5-HT4 binding data. In this study we analyse the performance of some fingerprint descriptors, metrics and hierarchical methods to classify compounds according to their activity.
Post subject: Advanced Automatic Generation of 3D Molecular Structures
Posted: Fri Jun 22, 2007 1:11 pm
Title: Advanced Automatic Generation of 3D Molecular Structures
Authors: Gábor Imre, Adrián Kalászi, Imre Jákli, Ödön Farkas
Institution:Laboratory of Chemical Informatics, Institute of Chemistry,
Eötvös Loránd University, 1/A Pázmány Péter sét., Budapest
Abstract: The efficiency of 3D structure based HTS (high throughput screening) tools also can be enhanced by employing conformational analysis to yield multiple valid structures.
Our approach utilizes a composition of several methods ranging from pure rule based1, multi dimensional distance geometry method2 to stored substructure lookup features in a flexible software framework. The actual implementation is a highly portable JAVA software, which fits in a broad scale of applications: it can be used in small web drawing applets3 as well as a standalone database processing component.
Post subject: JChem Cartridge: Cheminformatics Platform for Oracle
Posted: Fri Jun 22, 2007 1:49 pm
Title: JChem Cartridge: Cheminformatics Platform for Oracle
Authors: Peter Kovacs, Szilard Dorant, Szabolcs Csepregi, Nora Mate, Gyorgy Pirok, Ferenc Csizmadia
Institution: ChemAxon
Abstract: JChem Cartridge adds chemical knowledge to the Oracle platform. Data can be searched by structure, substructure and similarity criteria through extending Oracle's native SQL language. Chemical data can be easily inserted and modified using SQL.
JChem Cartridge relies on Oracle's extensible indexing framework for best search performance. In order to take advantage of this capability, the index type has to be applied.
Title: Standardizer - Molecular Cosmetics for Chemoinformatics
Authors: György Pirok, Nora Mate, Istvan Cseh, Attila Szabo, Szilard Dorant, Peter Kovacs, Szabolcs Csepregi, Alex Allardyce, Ferenc Csizmadia
Institution: ChemAxon
Abstract: A chemical compound can appear in various forms and its graphical representation often depends on the taste of the chemist. These variants are usually represented with different graphs in chemical software programs making the structural identification difficult. Apart from the naturally occurring mesomeric and tautomeric issues, chemical compounds are rarely neutral and pure, thus counterions and solvents might appear in the chemical structure files making the identification even more problematic. ChemAxon1 developed Standardizer, a Java-based software tool for the batch conversion of chemical structures according to a standard defined by the chemical database administrator.
Presentation:http://www.chemaxon.com/conf/Standardizer.pdf
Title: A method for calculating the pKa values of small and large molecules
Authors: József Szegezdi, Ferenc Csizmadia
Institution: ChemAxon
Abstract: A method was developed for predicting of the aqueous ionization constants (pK ) of organic molecules. The method is a based on empirically calculated physico-chemical parameters that are obtained from ionization site-specific regression equations.
Title: Community-based approach to research on infectious diseases of the developing world and global health
Authors: Rita Stanikunaite PhD, Arnas Palaima PhD, Barry A. Bunin PhD
Institution: Collaborative Drug Discovery (CDD, Inc.)
Abstract: Currently, infectious diseases of the developing world (e.g., malaria, tuberculosis) represent a global health challenge of the 21st century and require new approaches that would allow scientists to do research more effectively. As a result of the development of web-database technologies, recently a community-based approach to research on infectious diseases of the developing world and global health has emerged. The major components of effective scientific community include: (1) unifying goal, or focus on common therapeutic areas/diseases; (2) multiple research areas/expertise; (3) uniform database platform that allows effective data accumulation and management; (4) easy access and sharing of information; (5) potential for unlimited growth. The Collaborative Drug Discovery (CDD) database built by utilizing community-based web technologies currently provides a platform that allows scientists to archive, mine, and share research data with a focus on infectious diseases of the developing world. This new collaborative technology allows researchers to build up networks of technical experts around therapeutic or target areas thus facilitating discovery of new drug candidates. It allows scientists to speed up the research by sharing unpublished data providing new hope in the race to overcome drug resistance. An example illustrating how potential chemosensitizers to address chloroquine resistance could be identified by using the CDD database platform is presented..
Title: J-STRIKE™ : Structure Information and Knowledge Explorer
Web-based compound database management system
Author: Takahiro Ohshima
Institution: Infocom Corporation
Abstract: Compound database management system is the critical component of the drug discovery research in pharmaceutical companies, for all the information related to drug discovery workflow is centralized to the system. The identifier of a synthesized compound uniquely generated from the database system should be used in the following drug discovery workflow, and should be linked to other systems seamlessly. We, INFOCOM, developed a next generation compound database management system (J-STRIKE) by utilizing ChemAxon’s JChem toolkits and our know-how accumulated through drug discovery systems integration in
pharmaceutical companies for more than 20 years. We will describe J-STRIKE and how we integrate J-STRIKE with other systems such as assay database system, ActivityBase, data-mining system, Spotfire and others.
Post subject: BCS (Biopharmaceutics Classification System)
Posted: Fri Jun 22, 2007 2:22 pm
Title: Using ChemAxon tools In evaluating compounds for BCS(Biopharmaceutics Classification System) in ADME (Absorption, Distribution, Metabolism, Excreation)
Authors: Yoichiro Hamazaki,Atsuro Takahashi
Institution: Infocom Corporation
Abstract: In recent years, it has become common to evaluate the ADME characteristics in the early stage of the drug discovery process. One of the methods is high throughput screening (HTS) such as PAMPA and Caco-2. HTS is useful, but it has some problems. One of the major problems is that there is no established reference database. The other is the lack of feedback of the knowledge of relationships between ADME characteristics and molecular structures, even though lots of data has been generated and accumulated. We developed a web-based proto-type system using JChem toolkits to provide the BCS evaluation using a reference database, The ADME INDEX from Lighthouse Data Solutions, LLC, and the fragmental analysis between ADME characteristicand molecular structures. In the BCS evaluation, we tried In Combo concept to bridge experimental conditions between different labs. With such concept,we believe our prediction of BCS classification becomes more realistic than typical In Silico predictive software. In the fragmental analysis, user canget an insight which fragments have impact on the permeability and solubility improvement, which is critical to the BCS classification.
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