生物信息学在蛋白质组学上的应用

(,210009),3,;;;;Q51A0517-6611(2006)23-6142-03ApplicationofBio-informaticsinProteomicsHUANGXiao(SchoolofLifeScienceandTechnology,ChinaPharmaceuticalUniversity,Nanjing,Jiangsu210009)AbstractProteomicsisanewsymbolicresearchfieldofthepost-genomictime.Itsrapiddevelopmentdependsheavilyonthedynamicgrowthofbioin-formatics.Recentadvancesintheapplicationofbioinformaticsinproteomicswerediscussedfromthreeaspects:proteindatabases,proteinanalysisansdproteinfunction.KeywordsBioinformatics;Proteomics;Proteindatabase;Proteinanalysis;Proteinfunction,,,,,,,11.1(Bioinformatics),1987,,,,,,,,3:,DNA;,;,[1,2]1.2(Proteome)WilkinsWillians[3,4]1994,,[5,6],,,(1986-),,,,:2006-09-01,(Expres-sionprofile),,,[7]22.1Internet,,500,300,,42.1.12.1.2-DNA[8],:SWISS-PROTSWISS-PROTannotatedproteinsequencedatabase;PIR-internationalTheProteinInformationResource(proteinsequence);MIPSMartinsriedinstituteforproteinsequenceandhomologydataandyeastgenomeinformation;PROSITEPROSITEdictionaryofproteinsitesandpatterns;InterProIntegratedResourcesofPro-teinsDomainsandFunctionalSites;DOMOProteindomaindatabase(Automaticallygenerated)BLOCKS;PFAM;PRINTS;ProDom;PROTOMAP;SBASE;SMART;ProClass;Kabat;PMD,:WORLD-2DPAGE(Acompleteindexof2D-PAGEdatabaseandservers);Phoretixlinks(Phoretixpageoflinksto2Dgeldatabase)1[9]SCOP(Structuralclassificationofpro-,JournalofAnhuiAgri.Sci.2006,34(23):6142-6144teins[MirroratUSA|Israel|Singapore|Australia]);SWISS-MODEL(Repository-Automaticallygeneratedproteinmodelsdatabase);BioMagResBank(Repositoryfordataonproteins,pep-tides,andnucleicacidsfromNMRspectroscopy);PDB(ProteinDataBank[MirrorsinEBI])ModBase;CATH;MolRUs;BMMDomainServer;PRESAGE;ReLiBase;CCDC-CANSITE;ProNet;INTERACT;DIP,DNADPInteract(DNA-Proteinsinteractionsdatabase)1Biobase,(CebterforGenomeResearch)ECO2DBASE(NCBI)Heat2DPAGE()HSC2DPAGE(Harefield,HeartScienceCenter)LSB,(LargeScaleBiology)QUESTRef52,,(ColdSpringHarborLab)SWISS2DPAGE10,:,,,,,(,UniversityHospital)YEASTScerevisiae,Spombe(GoteborgUniversity)YEASTScerevisiae(Proteomeinc)2.1.3,,,PIR;MIPS;SWISS-PROT;TrEMBLE;GenPept,,,,NRDB;MIPSX;OWLSP+TrEM-BLE[10],,,BLOCKS;PROSITE;PFAM;PRINTS;ProDom;COGsSCOP;CATH;PDBsumPDB,GO3,KEGG;DIP;BIND;SPAD2.1.4Flybase[11];Wormbase[12];EcoCyc[13]2.2,,(2-DE[14,15]Edman),()42.2.120,ExPASy[16](ExPASySwiss-Prot;TrEMBL;EMBL,),AACompIdentSWISS-PROT,AACompIdent,pIMw()SWISS-PROT,6SWISS-PROTTrEM-BLAACompSim,AACompIdentSWISS-PROTPROPSEARCHExPASy,,,PROPSEARCH,PROPSEARCH,,2.2.2,,:ComputepI/MW()ExPASy,PIPK,,PeptideMass()ExPASy,,LysCArgCAspNGluC()TGREASE()FAS-TA,(,),,,SAPS(),,(/,,),2.2.3,341634233,ChouFasman;,;,,,nnPredict,FASTA/,H()E()(),65%,79%Predict-Protein,SWISS-PROT,MaxHomprofile,profile,PHD,1,72%,90%SSPREDPredictProtein,,,SOPMA,5,GORLevinPHDSOPMASOPMA,2.2.4,,,,threading:SWISS-MODEL()CPHmodels2.3,,,,,,,,[17],,,32002,,,,[1].[J].,2000(3):167-168.[2].[J].,2000(6):17-20.[3].[J].,1998,30(6):533-539.[4]WILKINSMR,PASQUAHC,APPELRD,etal.Fromproteinstoproteomes:largescaleproteinindentificationbytwo-dimensionalelectrophoresisandaminoacidanalysis[J].BioTechnology,1996,14:61-65.[5]GOULDKL,RENL,FEOKTISTOVAAS,etal.Tandemaffinitypurificationandidentificationofproteincomplexcomponents[J].Methods,2004,33(3):239-244.[6]CAUSIERB.Studyingtheinteractomewiththeyeasttwo-hybidsystemandmassspectrometry[J].MassSpectromRev,2004,23(5):350-367.[7],.[J].,2002,37(9):9-11.[8],,.[J].,2006(2):159-152.[9].[J].,2005(4):31-35.[10]KRIWENTSEVAEV,SERVANTF.APWEILERR.ImprovementstoCluSTr:thedatabaseofSWISS-PROT+TrEMBLproteinclusters[J].NucleicAcidsRes,2003,31:388-389.[11]DRYSDALERA.Flybase:genesandgenemodels[J].NucleicAcidsResDatabaseIssue,2005,33:390-395.[12]CHENN.Wormbase:acomprehensivedataresourceforCaenorhabditisbiologyandgenomics[J].NucleicAcidsResDatabaseIssue,2005,33:383-389.[13]KESELERIM.EcoCye:acomprehensivedatabaseresourceforEscherichiacoli[J].NucleicAcidsResDatabaseIssue,2005,33:334-337.[14]LEFKOVITSI.Functionalandstructuralproteomics:acriticalappraisal[J].JournalofChromatographyB,2003,787:1-10.[15],.[J].,2005(8):4-6.[16],.[J].,2005,12(12):909-912.[17]HAGENJB.Theoriginsofbioinformatics[J].NatRevGenet,2002,1:231-236.(6115),,,EC50,[1].[M].:,2002:448-451.[2].[M].:,1994:39-44.[3],.6[J].,1994(1):8.[4],.(II)[J].,2000(31):105-107.44162006