Efficient Prediction of Co-Complexed Proteins Based on Coevolution 英文参考文献.docVIP

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Efficient Prediction of Co-Complexed Proteins Based on Coevolution 英文参考文献.doc

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Efficient Prediction of Co-Complexed Proteins Based on Coevolution 英文参考文献

EfficientPredictionofCo-ComplexedProteinsBasedon Coevolution DamienM.deVienne1,2*,Je′ro?meAze′3 1Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona, Spain, 2Universitat Pompeu Fabra, Barcelona, Spain, 3UMR CNRS 8623, LaboratoiredeRechercheenInformatique,Universite′ Paris-Sud,Orsay,France Abstract The prediction of the network of protein-protein interactions (PPI) of an organism is crucial for the understanding of biologicalprocessesandforthedevelopmentofnewdrugs.Machinelearningmethodshavebeensuccessfullyappliedto the prediction of PPI in yeast by the integration of multiple direct and indirect biological data sources. However, experimentaldataarenotavailableformostorganisms.Weproposehereanensemblemachinelearningapproachforthe predictionofPPIthatdependssolelyonfeaturesindependentfromexperimentaldata.Wedevelopednewestimatorsofthe coevolution between proteins and combined them in an ensemble learning procedure. We applied this method to a datasetofknownco-complexedproteinsinEscherichiacoliandcomparedittopreviouslypublishedmethods.Weshow thatourmethodallowspredictionofPPIwithanunprecedentedprecisionof95.5%forthefirst200sortedpairsofproteins comparedto28.5%onthesamedatasetwiththepreviousbest method. Acloseinspection ofthebest predictedpairs allowedustodetectneworrecentlydiscoveredinteractionsbetweenchemotacticcomponents,theflagellarapparatusand RNApolymerasecomplexesinE.coli. Citation: de Vienne DM, Aze′ J (2012) Efficient Prediction of Co-Complexed Proteins Based on Coevolution. PLoS ONE 7(11): e48728. doi:10.1371/ journal.pone.0048728 Editor:MortenNielsen,TechnicalUniversityofDenmark,Denmark ReceivedJune14,2012;AcceptedSeptember28,2012;PublishedNovember9,2012 Copyright: ? 2012 de Vienne, Aze′. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:Theworkwas