Predicting Turns in Proteins with a Unified Model 英文参考文献.docVIP

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Predicting Turns in Proteins with a Unified Model 英文参考文献.doc

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Predicting Turns in Proteins with a Unified Model 英文参考文献

PredictingTurnsinProteinswithaUnifiedModel QiSong,TonghuaLi*,PeishengCong,JiangmingSun,DapengLi,ShengnanTang DepartmentofChemistry,TongjiUniversity,Shanghai,China Abstract Motivation:Turnsareacriticalelementofthestructureofaprotein;turnsplayacrucialroleinloops,folds,andinteractions. Currentpredictionmethodsarewelldevelopedforthepredictionofindividualturntypes,includinga-turn,b-turn,andc- turn,etc.However,forfurtherproteinstructureandfunctionpredictionitisnecessarytodevelopauniformmodelthatcan accuratelypredictalltypesofturnssimultaneously. Results:Inthisstudy,wepresentanovelapproach,TurnP,whichofferstheabilitytoinvestigatealltheturnsinaprotein basedonaunifiedmodel.ThemaincharacteristicsofTurnPare:(i)usingnewlyexploitedfeaturesofstructuralevolution information(secondarystructureandshapestringofprotein)basedonstructurehomologies,(ii)consideringalltypesof turnsinaunifiedmodel,and(iii)practicalcapabilityofaccuratepredictionofallturnssimultaneouslyforaquery.TurnP utilizes predicted secondary structures and predicted shape strings, both of which have greater accuracy, based on innovativetechnologieswhichwerebothdevelopedbyourgroup.Then,sequenceandstructuralevolutionfeatures,which areprofileofsequence,profileofsecondarystructuresandprofileofshapestringsaregeneratedbysequenceandstructure alignment.WhenTurnPwasvalidatedonanon-redundantdataset(4,107entries)byfive-foldcross-validation,weachieved anaccuracyof88.8%andasensitivityof71.8%,whichexceededthemoststate-of-the-artpredictorsofcertaintypeofturn. Newlydeterminedsequences,theEVAandCASP9datasetswereusedasindependenttestsandtheresultsweachieved wereoutstandingforturnpredictionsandconfirmedthegoodperformanceofTurnPforpracticalapplications. Citation: Song Q, Li T, Cong P, Sun J, Li D, et al. (2012) Predicting Turns in Proteins with a Unified Model. PLoS ONE 7(11): e48389. doi:10.1371/ journal.pone.0048389 Editor:GajendraP.S.Raghava,CSIR-InstituteofMicrobialTechnology,India ReceivedJune22,2012;AcceptedSeptember24,2012;Publishe