Prediction of Carbohydrate Binding Sites on Protein Surfaces with 3-Dimensional Probability Density Distributions of Interacting Atoms 英文参考文献.docVIP

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Prediction of Carbohydrate Binding Sites on Protein Surfaces with 3-Dimensional Probability Density Distributions of Interacting Atoms 英文参考文献.doc

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Prediction of Carbohydrate Binding Sites on Protein Surfaces with 3-Dimensional Probability Density Distributions of Interacting Atoms 英文参考文献

PredictionofCarbohydrateBindingSitesonProtein Surfaceswith3-DimensionalProbabilityDensity DistributionsofInteractingAtoms Keng-ChangTsai1¤,Jhih-WeiJian1,3,4,Ei-WenYang1,2,Po-ChiangHsu1,Hung-PinPeng1,3,4 ,Ching- TaiChen1,3,5,Jun-BoChen1,6,Jeng-YihChang1,Wen-LianHsu2,An-SueiYang1* 1Genomics Research Center, Academia Sinica, Taipei, Taiwan, 2Institute of Information Sciences, Academia Sinica, Taipei, Taiwan, 3Bioinformatics Program, Taiwan InternationalGraduateProgram,InstituteofInformationScience,AcademiaSinica,Taipei,Taiwan,4InstituteofBiomedicalInformatics,NationalYang-MingUniversity, Taipei,Taiwan,5InstituteofBioinformaticsandSystemsBiology,NationalChiao-TungUniversity,Hsinchu,Taiwan,6DepartmentofComputerScience,NationalTsing- HuaUniversity,Hsinchu,Taiwan Abstract Non-covalent protein-carbohydrate interactions mediate molecular targeting in many biological processes. Prediction of non-covalent carbohydrate binding sites on protein surfaces not only provides insights into the functions of the query proteins;informationonkeycarbohydrate-bindingresiduescouldsuggestsite-directedmutagenesisexperiments,design therapeutics targeting carbohydrate-binding proteins, and provide guidance in engineering protein-carbohydrate interactions. In this work, we show that non-covalent carbohydrate binding sites on protein surfaces can be predicted with relatively high accuracy when the query protein structures are known. The prediction capabilities were based on a novelencodingschemeofthethree-dimensionalprobabilitydensitymapsdescribingthedistributionsof36non-covalent interactingatomtypesaroundproteinsurfaces.Onemachinelearningmodelwastrainedforeachofthe30proteinatom types.Themachinelearningalgorithmspredictedtentativecarbohydratebindingsitesonqueryproteinsbyrecognizing the characteristic interacting atom distribution patterns specific for carbohydrate binding sites from known protein structures.Thepredictionresultsforallproteinatomtypeswereintegratedintosurfacepatchesastentativeca