Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure 英文参考文献.docVIP

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Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure 英文参考文献.doc

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Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure 英文参考文献

PredictingProteinLigandBindingSitesbyCombining EvolutionarySequenceConservationand3DStructure JohnA.Capra1,2,RomanA.Laskowski3,JanetM.Thornton3,MonaSingh1,2*,ThomasA.Funkhouser1* 1Department ofComputer Science,PrincetonUniversity,Princeton,NewJersey,UnitedStatesofAmerica, 2Lewis-SiglerInstitute forIntegrativeGenomics,Princeton University,Princeton,NewJersey,UnitedStatesofAmerica,3EuropeanBioinformaticsInstitute,WellcomeTrustGenomeCampus,Hinxton,Cambridge,UnitedKingdom Abstract Identifying a protein’s functional sites is an important step towards characterizing its molecular function. Numerous structure- and sequence-based methods have been developed for this problem. Here we introduce ConCavity, a small molecule binding site prediction algorithm that integrates evolutionary sequence conservation estimates with structure- based methods for identifying protein surface cavities. In large-scale testing on a diverse set of single- and multi-chain protein structures, we show that ConCavity substantially outperforms existing methods for identifying both 3D ligand binding pockets and individual ligand binding residues. As part of our testing, we perform one of the first direct comparisons of conservation-based and structure-based methods. We find that the two approaches provide largely complementaryinformation,whichcanbecombinedtoimproveuponeitherapproachalone.Wealsodemonstratethat ConCavityhasstate-of-the-artperformanceinpredictingcatalyticsitesanddrugbindingpockets.Overall,thealgorithms and analysis presented here significantly improve our ability to identify ligand binding sites and further advance our understandingoftherelationshipbetweenevolutionarysequenceconservationandstructuralandfunctionalattributesof proteins. Data, source code, and prediction visualizations are available on the ConCavity web site (http://compbio.cs. /concavity/). Citation:CapraJA,LaskowskiRA,ThorntonJM,SinghM,FunkhouserTA(2009)PredictingProteinLigandBindingSitesbyCombiningEvolutionarySequ