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WIREs Comput Mol Sci
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Computational chemogenomics

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Abstract Chemogenomics is a new interdisciplinary research field aiming at the genome‐wide systematic identification, expansion, analysis, and prediction of ligand–protein interactions using both in vitro and in silico approaches. Computational chemogenomics integrates the aspects of chemoinformatics and bioinformatics and aims to provide adequate molecular information systems for chemogenomics data and techniques for both ligand‐based and structure‐based data analysis and predictive modeling. The knowledge‐based exploration of the ligand‐target SAR matrix—the chemogenomics knowledge space—will help to discover and validate an increased number of small‐molecule compounds and postulated disease targets earlier and faster. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 57–67 DOI: 10.1002/wcms.11 This article is categorized under: Structure and Mechanism > Molecular Structures Computer and Information Science > Chemoinformatics

GeneGo pathway map neurophysiological process dopamine–D2 receptor signaling in central nervous system. Compounds are represented by hexagons, proteins by solid shapes, and enzymatic reactions by rectangles. Protein–protein, compound–protein, and compound–reaction interactions are shown as unidirectional arrows.12 (Reproduced with permission from Ref 53. Copyright 2009. GeneGo and Springer).

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General representation of the complete chemogenomics matrix as implemented in the pocketome engine.53 Each column, P1, P2, … represents a conformational ensemble of a protein pocket. Each row represents a chemical compound. The goal of the pocketome structural chemogenomics engine is to report, if experimental data are available, or predict the following: (1) the binding geometry of each compound to the pockets it can bind and (2) an estimate of the binding free energy, eij. Although the screening application searching for potential binders among virtual or available chemicals is widely used, comparing eij for the same compound with different pockets (or proteins), also known as specificity profiling, requires new approaches. (Reproduced with permission from Ref 53. Copyright 2009 Genego and Springer).

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Structure and Mechanism > Molecular Structures

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