Predicting Residue-Residue Contacts and Helix-Helix Interactions in Transmembrane Proteins Using an Integrative Feature-Based Random Forest Approach 英文参考文献.docVIP

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Predicting Residue-Residue Contacts and Helix-Helix Interactions in Transmembrane Proteins Using an Integrative Feature-Based Random Forest Approach 英文参考文献.doc

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Predicting Residue-Residue Contacts and Helix-Helix Interactions in Transmembrane Proteins Using an Integrative Feature-Based Random Forest Approach 英文参考文献

PredictingResidue-ResidueContactsandHelix-Helix InteractionsinTransmembraneProteinsUsingan IntegrativeFeature-BasedRandomForestApproach Xiao-FengWang1,ZhenChen1,ChuanWang1,Ren-XiangYan1,ZidingZhang1*,JiangningSong2,3* 1StateKeyLaboratoryofAgrobiotechnology,CollegeofBiologicalSciences,ChinaAgriculturalUniversity,Beijing,China,2StateEngineeringLaboratoryforIndustrial EnzymesandKeyLaboratoryofSystemsMicrobialBiotechnology,TianjinInstituteofIndustrialBiotechnology,ChineseAcademyofSciences,Tianjin,China,3Department ofBiochemistryandMolecularBiology,FacultyofMedicine,MonashUniversity,Melbourne,Victoria,Australia Abstract Integralmembraneproteinsconstitute25–30%ofgenomesandplaycrucialrolesinmanybiologicalprocesses.However, lessthan1%ofmembraneproteinstructuresareintheProteinDataBank.Inthiscontext,itisimportanttodevelopreliable computational methods for predicting the structures of membrane proteins. Here, we present the first application of randomforest(RF)forresidue-residuecontactpredictionintransmembraneproteins,whichwetermasTMhhcp.Rigorous cross-validationtestsindicatethatthebuiltRFmodelsprovideamorefavorablepredictionperformancecomparedwith twostate-of-the-artmethods,i.e.,TMHconandMEMPACK.Usingastrictleave-one-protein-outjackknifingprocedure,they werecapableofreachingthetopL/5predictionaccuraciesof49.5%and48.8%fortwodifferentresiduecontactdefinitions, respectively. The predicted residue contacts were further employed to predict interacting helical pairs and achieved the Matthew’scorrelationcoefficientsof0.430and0.424,accordingtotwodifferentresiduecontactdefinitions,respectively.To facilitate the academic community, the TMhhcp server has been made freely accessible at / tmhhcp. Citation:WangX-F,ChenZ,WangC,YanR-X,ZhangZ,etal.(2011)PredictingResidue-ResidueContactsandHelix-HelixInteractionsinTransmembraneProteins UsinganIntegrativeFeature-BasedRandomForestApproach.PLoSONE6(10):e26767.doi:10.1371/journal.pone.0026767 Editor:RubenClaudioAguilar,PurdueUniversity,UnitedSta