Generalized Fragment Picking in Rosetta Design, Protocols and Applications 英文参考文献.docVIP

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Generalized Fragment Picking in Rosetta Design, Protocols and Applications 英文参考文献.doc

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Generalized Fragment Picking in Rosetta Design, Protocols and Applications 英文参考文献

GeneralizedFragmentPickinginRosetta:Design, ProtocolsandApplications DominikGront1*,DanielW.Kulp2,RobertM.Vernon3,CharlieE.M.Strauss2,DavidBaker4 1FacultyofChemistry,UniversityofWarsaw,Warsaw,Poland,2LosAlamosNationalLaboratory,BioscienceDivision,LosAlamos,NewMexico,UnitedStatesofAmerica, 3PrograminMolecularStructureandFunction,HospitalForSickChildren,Toronto,Canada,4DepartmentofBiochemistry,HowardHughesMedicalInstitute,University ofWashington,Seattle,Washington,UnitedStatesofAmerica Abstract TheRosettadenovostructurepredictionandloopmodelingprotocolsbeginwithcoarsegrainedMonteCarlosearchesin whichthemovesarebasedonshortfragmentsextractedfromadatabaseofknownstructures.Herewedescribeanew objectorientedprogramforpickingfragmentsthatgreatlyextendsthefunctionalityofthepreviousprogram(nnmake)and opens the door for new approaches to structure modeling. We provide a detailed description of the code design and architecture, highlighting its modularity, and new features such as extensibility, total control over the fragment picking workflowandscoringsystemcustomization.Wedemonstratethattheprogramprovidesatleastasgoodbuildingblocksfor ab-initiostructurepredictionasthepreviousprogram,andprovideexamplesofthewiderangeofapplicationsthatarenow accessible. Citation:GrontD,KulpDW,VernonRM,StraussCEM,BakerD(2011)GeneralizedFragmentPickinginRosetta:Design,ProtocolsandApplications.PLoSONE6(8): e23294.doi:10.1371/journal.pone.0023294 Editor:VladimirN.Uversky,UniversityofSouthFloridaCollegeofMedicine,UnitedStatesofAmerica ReceivedApril22,2011;AcceptedJuly12,2011;PublishedAugust24,2011 Copyright: ? 2011 Gront et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding: DG was supported bya MarieCurie fellowship (FP7-people-IOF), project no.221081. Thefundershad norole in study design, data collection and analysis,