How a Structure-Centric Community for Chemists Can Benefit Drug Discovery - Virtual Screening Experiments Utilizing a Publicly Accessible Ligand Database, QSAR Modeling Tools and a Virtual Docking Software Package
by Antony Williams, ChemConnector on Sep 02, 2008
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ChemSpider is an online database of over 20 million chemical structures assembled from almost a hundred data sources including chemical and screening library vendors, publicly accessible databases and ...
ChemSpider is an online database of over 20 million chemical structures assembled from almost a hundred data sources including chemical and screening library vendors, publicly accessible databases and resources, commercial databases and Open Access literature articles. Such a public resource provides a rich source of ligands for the purpose of virtual screening experiments. These can take many forms. This work will present results from two specific types of studies: 1) Quantitative Structure Activity Relationship (QSAR) based analyses and 2) In-silico docking into protein receptor sites. We will review results from the application of both approaches to a number of specific examples using the software outlined below.
The QSAR analyses utilize the ChemModLab environment which is a free, web-based toolbox for fitting and assessing quantitative structure-activity relationships. Its elements include a cheminformatics front end to supply molecular descriptors, a set of statistical methods for fitting models, and methods for validating the resulting model. Five molecular descriptor sets are used with 16 math modeling methods to give a total of 80 QSAR models. The input is a file of compounds and a text file for biological activity.
The in-silico docking experiments are conducted using a combination QSAR/Docking approach using the SimBioSys eHITS and Lasso software programs. The docking procedure allows for the screening of a complete molecular database to obtain the correct binding poses and estimated binding affinities. The ligand based screening tool utilizes a novel conformation independent 3D QSAR descriptor, ideally suited for scaffold hopping.
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