dbPTM3.0(蛋白质翻译数据库)Publishedonline27November2021NucleicAcidsResearch,2021,Vol.41,DatabaseissueD295–D305doi:10.1093/nar/gks1229dbPTM3.0:aninformativeresourceforinvestigatingsubstratesitespecificityandfunctionalassociationofproteinpost-translationalmodificationsCheng-TsungLu1,Kai-YaoHuang1,Min-GangSu1,Tzong-YiLee1,2,*,NeilArvinBretana1,Wen-ChiChang3,Yi-JuChen4,Yu-JuChen4andHsien-DaHuang5,6,*1DepartmentofComputerScienceandEngineering,YuanZeUniversity,2GradulatePrograminBiomedicalInformatics,YuanZeUniversity,Chung-Li320,3InstituteofTropicalPlantSciences,NationalChengKungUniversity,Tainan701,4InstituteofChemistry,AcademiaSinica,Taipei115,5InstituteofBioinformaticsandSystemsBiologyand6DepartmentofBiologicalScienceandTechnology,NationalChiaoTungUniversity,Hsin-Chu300,TaiwanReceivedSeptember18,2021;RevisedOctober26,2021;AcceptedOctober31,2021ABSTRACTlocatedinprotein-interactingdomains.Additionally,Proteinmodificationisanextremelyimportanttheinformationofstructuraltopologiesontrans-post-translationalregulationthatadjuststhemembrane(TM)proteinsisintegratedindbPTMinphysicalandchemicalproperties,conformation,ordertodelineatethestructuralcorrelationbetweenstabilityandactivityofaprotein;thusalteringthereportedPTMsitesandTMtopologies.Tofacili-proteinfunction.DuetothehighthroughputoftatetheinvestigationofPTMsonTMproteins,themassspectrometry(MS)-basedmethodsinidentify-PTMsubstratesitesandthestructuraltopologyareingsite-specificpost-translationalmodificationsgraphicallyrepresented.Also,literatureinformation(PTMs),dbPTM(http://dbPTM.mbc.nctu.edu.tw/)isrelatedtoPTMs,orthologousconservationsandupdatedtointegrateexperimentalPTMsobtainedsubstratemotifsofPTMsarealsoprovidedinthefrompublicresourcesaswellasmanuallycuratedresource.Finally,thisversionfeaturesanimprovedMS/MSpeptidesassociatedwithPTMsfromwebinterfacetofacilitateconvenientaccesstotheresearcharticles.Version3.0ofdbPTMaimstoberesource.aninformativeresourceforinvestigatingthesub-stratespecificityofPTMsitesandfunctionalasso-ciationofPTMsbetweensubstratesandtheirINTRODUCTIONinteractingproteins.Inordertoinvestigatethesub-Proteinpost-translationalmodication(PTM)playsanstratespecificityformodificationsites,anewlyde-essentialroleinvariouscellularprocessesthatadjustsvelopedstatisticalmethodhasbeenappliedtothephysicalandchemicalproperties,folding,conform-identifythesignificantsubstratemotifsforeachation,stabilityandactivityofproteins;thusalteringtypeofPTMscontainingsufficientexperimentalproteinfunction(1).Morethan200differenttypesofdata.AccordingtothedatastatisticsindbPTM,PTMshavebeenidentiedbymassspectrometry(MS)-60%ofPTMsitesarelocatedinthefunctionalbasedproteomics(2).Thebiologicalfunctionsofthisdomainsofproteins.ItisknownthatmostPTMsubiquitousregulatorymechanismsincludephosphoryl-cancreatebindingsitesforspecificprotein-ationforsignaltransduction,attachmentoffattyacidsinteractiondomainsthatworktogetherforcellularformembraneanchoringandassociation,glycosylationfunction.Thus,thisupdateintegratesprotein–forchangingproteinhalf-life,targetingsubstrates,promo-tionofcell–cellandcell–matrixinteractions,acetylationproteininteractionanddomain–domaininteractionandmethylationofhistoneforgeneregulationandtodeterminethefunctionalassociationofPTMsitesubiquitylationforproteindegradation(3).Withthe*Towhomcorrespondenceshouldbeaddressed.Tel:+886346...