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Beta Atomic Contacts Identifying Critical Specific Contacts in Protein Binding Interfaces.doc

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Beta Atomic Contacts Identifying Critical Specific Contacts in Protein Binding Interfaces

BetaAtomicContacts:IdentifyingCriticalSpecific ContactsinProteinBindingInterfaces QianLiu*,CheeKeongKwoh,StevenC.H.Hoi* BIRC,SchoolofComputerEngineering,NanyangTechnologicalUniversity,Singapore,Singapore Abstract Specific binding between proteins plays a crucial role in molecular functions and biological processes. Protein binding interfacesandtheiratomiccontactsaretypicallydefinedbysimplecriteria,suchasdistance-baseddefinitionsthatonlyuse somethresholdofspatialdistanceinpreviousstudies.Thesedefinitionsneglectthenearbyatomicorganizationofcontact atoms,andthusdetectpredominantcontactswhichareinterruptedbyotheratoms.Itisquestionablewhethersuchkinds ofinterruptedcontactsareasimportantasothercontactsinproteinbinding.Totacklethischallenge,weproposeanew definitioncalledbeta(b)atomiccontacts.Ourdefinition,foundedontheb-skeletonsincomputationalgeometry,requires thatthereisnootheratominthecontactspheresdefinedbytwocontactatoms;thissphereissimilartothevanderWaals spheresofatoms.Thestatisticalanalysisonalargedatasetshowsthatbcontactsareonlyasmallfractionofconventional distance-basedcontacts.Toempiricallyquantifytheimportanceofbcontacts,wedesignbACV,anSVMclassifierwithb contactsasinput,toclassifyhomodimersfromcrystalpacking.WefoundthatourbACVisabletoachievethestate-of-the- artclassificationperformancesuperiortoSVMclassifierswithdistance-basedcontactsasinput.OurbACValsooutperforms several existing methods when being evaluated on several datasets in previous works. The promising empirical performancesuggeststhatbcontactscantrulyidentifycriticalspecificcontactsinproteinbindinginterfaces.bcontacts thus provide a new model for more precise description of atomic organization in protein quaternary structures than distance-basedcontacts. Citation: Liu Q, Kwoh CK, Hoi SCH (2013) Beta Atomic Contacts: Identifying Critical Specific Contacts in Protein Binding Interfaces. PLoS ONE 8(4): e59737. doi:10.1371/journal.pone.0059737 Editor:FrancaFraternali,King’sCollegeLondon,UnitedKingdom Re