Sybyl操作

IntroductiontoReceptorIntroductiontoReceptor--LigandLigandModelingusingSybylModelingusingSybylYukShamSupercomputingInstituteConsultantPhone:[phone]Email:[e-mail]•IntroductiontoSybyl–WhatisSybyl–Sybylfeatures–HowtorunSybyl•Examples–Buildingamolecule–Viewingaproteininpdbfileformat–Patchingupyourproteinmolecule–Minimization/MolecularDynamicSimulation–DockingaligandWhatisSybylWhatisSybyl•CommerciallyavailablefromTripos,Inc.SoftwareforresearchinLifeSciences.•SoftwareavailableontheSiliconGraphicsandLinuxWorkstations•Molecularvisualizationsoftwareforsmallchemicalandbiologicalmolecules•GraphicUserInterface(GUI)forotherstandalonesoftware(modules)HowtorunSybylHowtorunSybylI.RunningSybylfromtheconsolemoduleloadsybylsybylTheSybylviewerTheSybylviewerMSIlogoViewertoolbarFrequentlyUsedbuttonsModulesModulesModulesModulesSomenicefeaturesofSybylSomenicefeaturesofSybyl•Import/exportmultiplefileformat•Moleculeeditingandbuilding•I/Ointerfacetomultiplefileformat•Canhandlelargenumberofchemicalstructures•Easydefinitionandselectionoption•Highqualitygraphics•Exportcommandscripts•SavingyourenvironmentBuildingamoleculewithBuilderBuildingamoleculewithBuilder•Build/SketchMoleculeOptimizeamoleculestructureOptimizeamoleculestructure•Compute/MinimizeYouandyourmouseYouandyourmouse•Rightmouseclicktorotate•Middlemouseclicktotranslate•Leftandmiddlemouseclick(together)tochangethedepthcue•Middleandrightmouseclick(together)tozoominandout•DuringSelection:–MousepointatatomandleftmouseclicktoselectatomSearchingSearchingProteinDataBankProteinDataBank(PDB)(PDB)://(PDB)Atypicalfileformatforprotein(PDB)HEADERCALCIUM-BINDINGPROTEIN29-SEP-921CLL2COMPNDCALMODULIN(VERTEBRATE)1CLL3REMARK1REFERENCE11CLL13REMARK1AUTHW.E.MEADOR,A.R.MEANS,F.A.QUIOCHO1CLL14RORIGX20.0000000.0186590.0011550.000001CLL143..SEQRES1148ALAASPGLNLEUTHRGLUGLUGLNILEALAGLUPHELYS1CLL110SEQRES2148GLUALAPHESERLEUPHEASPLYSASPGLYASPGLYTHR1CLL111SEQRES3148ILETHRTHRLYSGLULEUGLYTHRVALMETARGSERLEU1CLL112..HELIX5VALA102ASN11111CLL134HELIX6VIASP118ALA12811CLL135HELIX7VIITYR138THR14611CLL136SHEET1S12ILE27THR2901CLL137SHEET2S12ILE63PHE65-1NILE63OILE271CLL138..ATOM1NLEU4-6.87321.08225.3121.0049.531CLL148ATOM2CALEU4-6.69622.00326.4471.0048.821CLL149ATOM3CLEU4-6.31823.39125.9291.0046.501CLL150ATOM4OLEU4-5.31323.98126.3521.0045.721CLL151ATOM5NTHR5-7.14723.87125.0131.0046.771CLL152ATOM6CATHR5-6.89125.19324.4281.0046.841CLL153...CONECT72472311371CLL1440CONECT73673511371CLL1441headersequencesec.structstructureinfo.connectivityDownloadDownloadHEADERCALCIUM-BINDINGPROTEIN29-SEP-921CLL2COMPNDCALMODULIN(VERTEBRATE)1CLL3REMARK1REFERENCE11CLL13REMARK1AUTHW.E.MEADOR,A.R.MEANS,F.A.QUIOCHO1CLL14RORIGX20.0000000.0186590.0011550.000001CLL143..SEQRES1148ALAASPGLNLEUTHRGLUGLUGLNILEALAGLUPHELYS1CLL110SEQRES2148GLUALAPHESERLEUPHEASPLYSASPGLYASPGLYTHR1CLL111SEQRES3148ILETHRTHRLYSGLULEUGLYTHRVALMETARGSERLEU1CLL112..HELIX5VALA102ASN11111CLL134HELIX6VIASP118ALA12811CLL135HELIX7VIITYR138THR14611CLL136SHEET1S12ILE27THR2901CLL137SHEET2S12ILE63PHE65-1NILE63OILE271CLL138..ATOM1NLEU4-6.87321.08225.3121.0049.531CLL148ATOM2CALEU4-6.69622.00326.4471.0048.821CLL149ATOM3CLEU4-6.31823.39125.9291.0046.501CLL150ATOM4OLEU4-5.31323.98126.3521.0045.721CLL151ATOM5NTHR5-7.14723.87125.0131.0046.771CLL152ATOM6CATHR5-6.89125.19324.4281.0046.841CLL153...CONECT72472311371CLL1440CONECT73673511371CLL1441headersequencesec.structstructureinfo.connectivityLoadingPDBfileinSybylLoadingPDBfileinSybylFile/ReadMixRendering:SelectingMixRendering:SelectingMixRendering:SelectingMixRendering:SelectingMixRendering:SelectingMixRendering:SelectingMixRenderingMixRenderingView/MixRenderingorView/BiopolymerDisplayBasicManipulationBasicManipulation•DeleteanObjectBuild/Zap•(un)displayanObjectView/(Un)displayView/Background/show•ChangeBackgroundcolorView/BackdropPatchingupyourproteinmoleculePatchingupyourproteinmoleculeBiopolymer/PrepareStructure/StructurePreparationTool/PatchingupyourproteinmoleculePatchingupyourproteinmoleculeBiopolymer/PrepareStructure/StructurePreparationTool/PatchingupyourproteinmoleculePatchingupyourproteinmoleculeBiopolymer/PrepareStructure/StructurePreparationTool/PatchingupyourproteinmoleculePatchingupyourproteinmoleculeBiopolymer/PrepareStructure/StructurePreparationTool/PatchingupyourproteinmoleculePatchingupyourproteinmoleculeBiopolymer/PrepareStructure/StructurePreparationTool/SavingyourenvironmentSavingyourenvironmentFile/SaveasSybylMol2fileformatSybylMol2fileformatFile/SaveasDefiningaregionDefiningaregionDefine/StaticSetDefiningaregionasasetDefiningaregionasasetDefine/StaticSetCreatemolecularsurfaceCreatemolecularsurfaceView/MOLCADSurface/MultiChannelSurfaceCreatemolecularsurfaceCreatemolecularsurfaceView/MOLCADSurface/MultiChannelSurfaceCreatemolecularsurfaceCreatemolecularsurfaceView/MOLCADSurface/MultiChannelSurfaceMov