PSPP A Protein Structure Prediction Pipeline for Computing Clusters 英文参考文献.docVIP

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PSPP A Protein Structure Prediction Pipeline for Computing Clusters 英文参考文献.doc

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PSPP A Protein Structure Prediction Pipeline for Computing Clusters 英文参考文献

PSPP:AProteinStructurePredictionPipelinefor ComputingClusters MichaelS.Lee1,2,3,RajkumarBondugula1,ValmikDesai1,NelaZavaljevski1,In-ChulYeh1 ,Anders Wallqvist1,JaquesReifman1* 1BiotechnologyHPCSoftwareApplicationsInstitute,TelemedicineandAdvancedTechnologyResearchCenter,U.S.ArmyMedicalResearchandMaterielCommand,Fort Detrick,Maryland,UnitedStatesofAmerica,2ComputationalandInformationSciencesDirectorate,U.S.ArmyResearchLaboratory,AberdeenProvingGround,Maryland, UnitedStatesofAmerica,3DepartmentofCellBiologyandBiochemistry,U.S.ArmyMedicalResearchInstituteofInfectiousDiseases,FortDetrick,Maryland,UnitedStates ofAmerica Abstract Background:Proteinstructuresarecriticalforunderstandingthemechanismsofbiologicalsystemsand,subsequently,for drugandvaccinedesign.Unfortunately,proteinsequencedataexceedstructuraldatabyafactorofmorethan200to1. Thisgapcanbepartiallyfilledbyusingcomputationalproteinstructureprediction.WhilestructurepredictionWebservers are a notable option, they often restrict the number of sequence queries and/or provide a limited set of prediction methodologies. Therefore, we present a standalone protein structure prediction software package suitable for high- throughput structural genomic applications that performs all three classes of prediction methodologies: comparative modeling, fold recognition, and ab initio. This software can be deployed on a user’s own high-performance computing cluster. Methodology/Principal Findings: The pipeline consists of a Perl core that integrates more than 20 individual software packagesanddatabases,mostofwhicharefreelyavailablefromotherresearchlaboratories.Thequeryproteinsequences arefirstdividedintodomainseitherbydomainboundaryrecognitionorBayesianstatistics.Thestructuresoftheindividual domainsarethenpredictedusingtemplate-basedmodelingorabinitiomodeling.Thepredictedmodelsarescoredwitha statistical potential andan all-atom force field. The top-scoring ab initio models areannotated by structural comparison againsttheStructuralC