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Page 1 of 1 (page number not for citation purposes) Chemistry Central Journal Open Access Poster presentation Information theory based scoring function for predicting protein-ligand binding affinity Mahesh Kulharia Address: MPI für molekulare Physiologie, 44227 Dortmund, Germany The development and validation of a new knowledge based scoring function (SIScoreJE) to predict binding affinity between proteins and ligands is presented. SIS- coreJE efficiently predicts the binding energy between a small molecule and its protein receptor. Protein-ligand atomic contact information was derived from a “nonre- dundant dataset” (NRD) of over 3000 X-ray crystal struc- tures of protein-ligand complexes. This information was classified for the individual “atom contact pairs” (ACP) according to a number of current atom-type classification schemes in addition to two of our own before calculating the atomic contact preferences. The preferences were cal- culated using an information theoretic relationship of joint entropy. Among 18 different atom-type classifica- tion schemes “ScoreJE atom type set2” (SATs2) was found to be most suitable for our approach. Single-body solva- tion potentials (SSP) were derived from the atomic con- tacts between the protein atom types and water molecules modelled using AQUARIUS2. Validation was carried out using an evaluation dataset of 100 protein-ligand com- plexes with known binding affinities. A combined SSP/ ScoreJE (SIScoreJE) performed significantly better than ScoreJE alone. Also SIScoreJE and ScoreJE performed bet- ter than GOLD::GoldScore, GOLD::ChemScore, and XScore. from 3rd German Conference on Chemoinformatics Goslar, Germany. 11-13 November 2007 Published: 26 March 2008 Chemistry Central Journal 2008, 2(Suppl 1):P44 doi:10.1186/1752-153X-2-S1-P44 <supplement> <title> <p>3rd German Conference on Chemoinformatics: 21. CIC-Workshop</p> </title> <note>Meeting abstracts - A single PDF containing all abstracts in this Supplement is available <a href="http://www.biomedcentral.com/content/files/pdf/1752-153X-2-S1-full.pdf">here</a>.</note> <url>http://www.biomedcentral.com/content/pdf/1752-153X-2-S1-info.pdf</url> </supplement> This abstract is available from: http://www.journal.chemistrycentral.com/content/2/S1/P44 © 2008 Kulharia

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Page 1: Information theory based scoring function for predicting protein-ligand binding affinity

Page 1 of 1(page number not for citation purposes)

Chemistry Central Journal

Open AccessPoster presentationInformation theory based scoring function for predicting protein-ligand binding affinityMahesh Kulharia

Address: MPI für molekulare Physiologie, 44227 Dortmund, Germany

The development and validation of a new knowledgebased scoring function (SIScoreJE) to predict bindingaffinity between proteins and ligands is presented. SIS-coreJE efficiently predicts the binding energy between asmall molecule and its protein receptor. Protein-ligandatomic contact information was derived from a “nonre-dundant dataset” (NRD) of over 3000 X-ray crystal struc-tures of protein-ligand complexes. This information wasclassified for the individual “atom contact pairs” (ACP)according to a number of current atom-type classificationschemes in addition to two of our own before calculatingthe atomic contact preferences. The preferences were cal-culated using an information theoretic relationship ofjoint entropy. Among 18 different atom-type classifica-tion schemes “ScoreJE atom type set2” (SATs2) was foundto be most suitable for our approach. Single-body solva-tion potentials (SSP) were derived from the atomic con-tacts between the protein atom types and water moleculesmodelled using AQUARIUS2. Validation was carried outusing an evaluation dataset of 100 protein-ligand com-plexes with known binding affinities. A combined SSP/ScoreJE (SIScoreJE) performed significantly better thanScoreJE alone. Also SIScoreJE and ScoreJE performed bet-ter than GOLD::GoldScore, GOLD::ChemScore, andXScore.

from 3rd German Conference on ChemoinformaticsGoslar, Germany. 11-13 November 2007

Published: 26 March 2008

Chemistry Central Journal 2008, 2(Suppl 1):P44 doi:10.1186/1752-153X-2-S1-P44

<supplement> <title> <p>3rd German Conference on Chemoinformatics: 21. CIC-Workshop</p> </title> <note>Meeting abstracts - A single PDF containing all abstracts in this Supplement is available <a href="http://www.biomedcentral.com/content/files/pdf/1752-153X-2-S1-full.pdf">here</a>.</note> <url>http://www.biomedcentral.com/content/pdf/1752-153X-2-S1-info.pdf</url> </supplement>

This abstract is available from: http://www.journal.chemistrycentral.com/content/2/S1/P44

© 2008 Kulharia

http://www.journal.chemistrycentral.com/content/2/S1/P44
http://www.biomedcentral.com/info/about/charter/

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