Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform 英文参考文献.docVIP

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Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform 英文参考文献.doc

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Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform 英文参考文献

GeneratingTriangulatedMacromolecularSurfacesby EuclideanDistanceTransform DongXu1,2,YangZhang1,2 * 1Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America, 2Center for Bioinformatics and DepartmentofMolecularBioscience,UniversityofKansas,Lawrence,Kansas,UnitedStatesofAmerica Abstract Macromolecularsurfacesarefundamentalrepresentationsoftheirthree-dimensionalgeometricshape.Accuratecalculation ofproteinsurfacesisofcriticalimportanceintheproteinstructuralandfunctionalstudiesincludingligand-proteindocking andvirtualscreening.Incontrasttoanalyticalorparametricrepresentationofmacromolecularsurfaces,triangulatedmesh surfaceshavebeenprovedtobeeasytodescribe,visualizeandmanipulatebycomputerprograms.Here,wedevelopanew algorithm of EDTSurf for generating three major macromolecular surfaces of van der Waals surface, solvent-accessible surfaceandmolecularsurface,usingthetechniqueoffastEuclideanDistanceTransform(EDT).Thetriangulatedsurfacesare constructeddirectlyfromvolumetricsolidsbyaVertex-ConnectedMarchingCubealgorithmthatformstrianglesfromgrid points.Comparedtotheanalyticalresult,therelativeerrorofthesurfacecalculationsbyEDTSurfis,2–4%dependingon thegridresolution,whichis1.5–4timeslowerthanthemethodsintheliterature;andyet,thealgorithmisfasterandcosts less computer memory than the comparative methods. The improvements in both accuracy and speed of the macromolecular surface determination should make EDTSurf a useful tool for the detailed study of protein docking and structure predictions. Both source code and the executable program of EDTSurf are freely available at http://zhang. /EDTSurf. Citation: Xu D, Zhang Y (2009) Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform. PLoS ONE 4(12): e8140. doi:10.1371/ journal.pone.0008140 Editor:MarkusJ.Buehler,MassachusettsInstituteofTechnology,UnitedStatesofAmerica ReceivedAugust19,2009;AcceptedNovember9,2009;PublishedDecember2,2009 Copy