Prediction of Ligand Binding Using an Approach Designed to Accommodate Diversity in Protein-Ligand Interactions 英文参考文献.docVIP

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Prediction of Ligand Binding Using an Approach Designed to Accommodate Diversity in Protein-Ligand Interactions 英文参考文献.doc

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Prediction of Ligand Binding Using an Approach Designed to Accommodate Diversity in Protein-Ligand Interactions 英文参考文献

PredictionofLigandBindingUsinganApproach DesignedtoAccommodateDiversityinProtein-Ligand Interactions LorraineMarsh DepartmentofBiology,LongIslandUniversity,Brooklyn,NewYork,UnitedStatesofAmerica Abstract Computationaldeterminationofprotein-ligandinteractionpotentialisimportantformanybiologicalapplicationsincluding virtual screening for therapeutic drugs. The novel internal consensus scoring strategy is an empirical approach with an extended set of 9 binding terms combined with a neural network capable of analysis of diverse complexes. Like conventionalconsensusmethods,internalconsensusiscapableofmaintainingmultipledistinctrepresentationsofprotein- ligandinteractions.Inatypicalusethemethodwastrainedusingligandclassificationdata(binding/nobinding)forasingle receptor. The internal consensus analyses successfully distinguished protein-ligand complexes from decoys (r2, 0.895 for aseriesoftypicalproteins).Resultsaresuperiortoothertestedempiricalmethods.Invirtualscreeningexperiments,internal consensusanalysesprovideconsistentenrichmentasdeterminedbyROC-AUCandpROCmetrics. Citation:MarshL(2011)PredictionofLigandBindingUsinganApproachDesignedtoAccommodateDiversityinProtein-LigandInteractions.PLoSONE6(8): e23215.doi:10.1371/journal.pone.0023215 Editor:JieZheng,UniversityofAkron,UnitedStatesofAmerica ReceivedMay19,2011;AcceptedJuly12,2011;PublishedAugust10,2011 Copyright: ? 2011 Lorraine Marsh. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:Theseauthorshavenosupportorfundingtoreport. CompetingInterests:Theauthorhasdeclaredthatnocompetinginterestsexist. *E-mail:lmarsh@ Introduction interaction [5]. Drugscore is a knowledge based function [5]. Againthebasisofbindingdeterminationisverybroad,reflecting knowledgederivedfromatominteractionsinmanyenvironments. Empirical potential scoring functions follow