Automatic classification of protein structure by using Gauss integrals

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1、AutomaticclassificationofproteinstructurebyusingGaussintegralsPeterRøgen*andBorisFain*DepartmentofMathematics,TechnicalUniversityofDenmark,Building303,DK-2800KongensLyngby,Denmark;and†DepartmentofStructuralBiology,StanfordUniversity,Stanford,CA94305CommunicatedbyMichaelLevitt,StanfordUniversityScho

2、olofMedicine,Stanford,CA,October24,2002(receivedforreviewSeptember12,2002)Weintroduceamethodoflookingat,analyzing,andcomparing‘‘thoughsignificantprogresshasbeenmadeoverthepastproteinstructures.Thetopologyofaproteiniscapturedby30decade,afast,reliableandconvergentmethodforproteinnumbersinspiredbyVass

3、ilievknotinvariants.Toillustratethesim-structuralalignmentisnotyetavailable.’’Thedeficienciesofplicityandpowerofthistopologicalapproach,weconstructamea-currentmethodsarisefromtheirrelianceondistance-basedsure(scaledGaussmetric,SGM)ofsimilarityofproteinshapes.Under[RMSD;seeKabsch(3)]measuresofsimila

4、rity,andalsofromthismetric,proteinchainsnaturallyseparateintofoldclusters.Weusetheirconsequentrequirementforsequencealignment.SGMtoconstructanautomaticclassificationprocedurefortheRMSDisanexcellentmeasureofsimilarityfornearlyidenticalCATH2.4database.Themethodisveryfastbecauseitrequiresneitherstructu

5、res(5),butoncetheshapeoftwoproteinsbeginstoalignmentofthechainsnoranychainchaincomparison.Italsohasdiverge,RMSDloosesitseffectiveness.Twocompletelyunre-onlyoneadjustableparameter.Weassign95.51%ofthechainsintolatedproteinsmayhavealargeRMSD,butsomaytworelatedtheproperC(class),A(architecture),T(topolo

6、gy),andH(homologouschainswhichconsistofidenticalsubunitsorienteddifferentlysuperfamily)fold,findallnewfolds,anddetectnofalsegeometricwithrespecttoeachother.RMSDcannotdistinguishthefirstpositives.UsingtheSGM,wedisplayamapofthespaceoffoldscasefromthesecond.projectedontotwodimensions,showtherelativeloc

7、ationsoftheThisdrawbackisusuallyaddressedbyusingvarioussophisticatedmajorstructuralclasses,andzoomintothespaceofproteinstosequencealignmenttechniquesthatfindrelatedsubunits(6–11).showarchitecture,topology,a