Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes 英文参考文献.docVIP

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Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes 英文参考文献.doc

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Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes 英文参考文献

ProteinDockingbytheUnderestimationofFreeEnergy FunnelsintheSpaceofEncounterComplexes YangShen1,2,IoannisCh.Paschalidis2,3,4,PiroozVakili2,3,5,SandorVajda1* 1BioMolecularEngineeringResearchCenter,DepartmentofBiomedicalEngineering,BostonUniversity, Boston, Massachusetts,UnitedStatesofAmerica,2Centerfor InformationandSystemsEngineering,BostonUniversity,Boston,Massachusetts,UnitedStatesofAmerica,3DivisionofSystemsEngineering,BostonUniversity,Boston, Massachusetts, United States of America, 4Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America, 5DepartmentofMechanicalEngineering,BostonUniversity,Boston,Massachusetts,UnitedStatesofAmerica Abstract Similarly to protein folding, the association of two proteins is driven by a free energy funnel, determined by favorable interactions in some neighborhood of the native state. We describe a docking method based on stochastic global minimizationoffunnel-shapedenergyfunctionsinthespaceofrigidbodymotions(SE(3))whileaccountingforflexibilityof theinterfacesidechains.Themethod,calledsemi-definiteprogramming-basedunderestimation(SDU),employsageneral quadratic function to underestimate a set of local energy minima and uses the resulting underestimator to bias further sampling.WhileSDUeffectivelyminimizesfunctionswithfunnel-shapedbasins,itsapplicationtodockingintherotational andtranslationalspaceSE(3)isnotstraightforwardduetothegeometryofthatspace.Weintroduceastrategythatuses separateindependentvariablesforside-chainoptimization,center-to-centerdistanceofthetwoproteins,andfiveangular descriptorsoftherelativeorientationsofthemolecules.Theremovalofthecenter-to-centerdistanceturnsouttovastly improve the efficiency of the search, because the five-dimensional space now exhibits a well-behaved energy surface suitable for underestimation. This algorithm explores the free energy surface spanned by encounter complexes that correspond to localfree energy minimaand shows simila