Estimating Absolute Configurational Entropies of Macromolecules The Minimally Coupled Subspace Approach 英文参考文献.docVIP

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Estimating Absolute Configurational Entropies of Macromolecules The Minimally Coupled Subspace Approach 英文参考文献.doc

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Estimating Absolute Configurational Entropies of Macromolecules The Minimally Coupled Subspace Approach 英文参考文献

EstimatingAbsoluteConfigurationalEntropiesof Macromolecules:TheMinimallyCoupledSubspace Approach UlfHensen1,OliverF.Lange2*,HelmutGrubmu¨ller1 1DepartmentofTheoreticalandComputationalBiophysics,Max-PlanckInstituteforBiophysicalChemistry,Go¨ttingen,Germany,2DepartmentofBiochemistry,University ofWashington,Seattle,Washington,UnitedStatesofAmerica Abstract Wedevelopageneralminimallycoupledsubspaceapproach(MCSA)tocomputeabsoluteentropiesofmacromolecules, suchasproteins,fromcomputergeneratedcanonicalensembles.Ourapproachovercomeslimitationsofcurrentestimates suchasthequasi-harmonicapproximationwhichneglectsnon-linearandhigher-ordercorrelationsaswellasmulti-minima characteristicsofproteinenergylandscapes.Here,FullCorrelationAnalysis,adaptivekerneldensityestimation,andmutual information expansions are combined and high accuracy is demonstrated for a number of test systems ranging from alkanestoa14residuepeptide.Wefurthercomputedtheconfigurationalentropyforthefull67-residuecofactorofthe TATAboxbindingproteinillustratingthatMCSAyieldsimprovedresultsalsoforlargemacromolecularsystems. Citation: Hensen U, Lange OF, Grubmu¨ller H (2010) Estimating Absolute Configurational Entropies of Macromolecules: The Minimally Coupled Subspace Approach.PLoSONE5(2):e9179.doi:10.1371/journal.pone.0009179 Editor:Jo¨rgLangowski,GermanCancerResearchCenter,Germany ReceivedMay10,2009;AcceptedJanuary25,2010;PublishedFebruary23,2010 Copyright: ? 2010 Hensen 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:U.H.wassupportedbytheDeutscheForschungsgemeinschaft(researchtraininggroup782).O.F.L.wassupportedbytheHumanFrontiersofScience Program and by the Volkswagen Foundation, Grant I/80436. The funders had no role in study design, data collection and analysis, decision to publish, or preparationofthemanuscript. CompetingI