Prediction of Protein–Protein Interaction Sites in Sequences and 3D Structures by Random Forests 英文参考文献.docVIP

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Prediction of Protein–Protein Interaction Sites in Sequences and 3D Structures by Random Forests 英文参考文献.doc

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Prediction of Protein–Protein Interaction Sites in Sequences and 3D Structures by Random Forests 英文参考文献

PredictionofProtein–ProteinInteractionSitesin Sequencesand3DStructuresbyRandomForests MileSikicˇ ′1*,SanjaTomic′2,KristianVlahovicˇek3* 1DepartmentofElectronicSystemsandInformationProcessing,FacultyofElectricalEngineeringandComputing,UniversityofZagreb,Zagreb,Croatia,2RudjerBosˇkovic′ Institute,Zagreb,Croatia,3BioinformaticsGroup,DepartmentofMolecularBiology,DivisionofBiology,FacultyofScience,UniversityofZagreb,Zagreb,Croatia Abstract Identifyinginteractionsitesinproteinsprovidesimportantcluestothefunctionofaproteinandisbecomingincreasingly relevantintopicssuchassystemsbiologyanddrugdiscovery.Althoughtherearenumerouspapersonthepredictionof interactionsitesusinginformationderivedfromstructure,thereareonlyafewcasereportsonthepredictionofinteraction residuesbasedsolelyonproteinsequence.Here,aslidingwindowapproachiscombinedwiththeRandomForestsmethodto predict protein interaction sites using (i) a combination of sequence- and structure-derived parameters and (ii)sequence informationalone.Forsequence-basedpredictionweachievedaprecisionof84%witha26%recallandanF-measureof40%. Whencombinedwithstructuralinformation,thepredictionperformanceincreasestoaprecisionof76%andarecallof38% withanF-measureof51%.Wealsopresentanattempttorationalizetheslidingwindowsizeanddemonstratethatanine- residuewindowisthemostsuitableforpredictorconstruction.Finally,wedemonstratetheapplicabilityofourprediction methodsbymodelingtheRas–Rafcomplexusingpredictedinteractionsitesastargetbindinginterfaces.Ourresultssuggest thatitispossibletopredictproteininteractionsiteswithquiteahighaccuracyusingonlysequenceinformation. Citation:Sikicˇ ′M,Tomic′S,VlahovicekK(2009)PredictionofProtein–ProteinInteractionSitesinSequencesand3DStructuresbyRandomForests.PLoSComput ˇ Biol5(1):e1000278.doi:10.1371/journal.pcbi.1000278 Editor:GaryD.Stormo,WashingtonUniversity,UnitedStatesofAmerica ReceivedJuly18,2008;AcceptedDecember16,2008;PublishedJanuary30,2009 Copyright:?2009Sikicˇ ′etal.Thisisanopen-accessarticledistribut