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1、本文以INGAP為例,闡述使用DS對某個蛋白從建模到動力學模擬,到結(jié)果分析的流程示意圖。一同源建模1.導入目標序列2.搜尋模板AnJI.RunX-廿二7?DplySLylB.?frIKtWQPiltsBuildUL>iEdittTuclticAcid.UntitkedlBu.ildul-1Eds1FtE-iaiaGLHDP5HGTLPFJG勺BLASTS-archNCENELPVCKFKY4-arahj4ijQAnc4-;'t>yuiriLlAriLyfSI-IUfil亂ifcbL.PretardNme吐tuw匚MILClJ-”BLA$TSerdiNa+JBLASTSear
2、ch*AnAkrHTrAic:ftnKijSimulationKeceiht4-LigandlataiactionsPhaEBacGfihcreStalllolftculsItcrq.iltc-SiailvriI7Se-arcb日'丄丁FOalLTiHDI.LhlsXHl再曰也H4ToqLlQBuildHon-iolagyhNa+1AlighE-equenceto|QjMq騎河芮也3lhw詒!MMVS.5.0J.215S可AnalyzeIrajectOK回詫&+Xl.ndly-zeiraje-d:口>回Vts玖GuildHcmolngyN口No亠.AlignSequenc
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14、亡ud.«rHAJT5亡arrb.OOIEexyfr)Stltetctntaract亡kiisft也tk亡prrtpntmdImJEtTUJtTirm血”AliffwmiUnctfeai嚴LuKatHrtiarFffi"NC5eIeGVilt:W555E555AT.¥1W1G5¥"¥UWIGLHDLHDalndl*;SLUaLsili.CacLCtlParjrnpbrrNampParamr'trir'i.i'iBlue-InputRnlodel站quinceUntrtJedldUntdedl】nput"
15、;femphtetrudurMlU70ATv1ffbfeSCreateSequenceProFileRaise上ilinStrudturefTrueShtvFxrm-iLarK«lpTFV-lVF5.構(gòu)建模型Sludio寸5BulIJ.«ndEJltHutL-aicMidBuild,xndEditPr&t<tnCtliA*!Hh-kIc-cFlc-ihlsniIdHibdIoyNdLiIx<血*PratucolName:Tsri£jr岸口LrtttdLLTAMLrrtiedDbli0PxaLblti(luwyOtrlin亡Ibl百h&s
16、亡三Fre-Ivsji.E«pwh.Prsj-irtTtoleini3ia.ulajtiQn|KcceM0r-Li®aid1strxitici皿斷FIlaj:atGe著孫uullIclBEUleEFTaaliQiUlpiaridn«l4£4>IU4Tf:4Enhly-EBJ'fqIi-ld.Ccm-irvaiLiSuperinbpiystFrot亡LiraTii>ltemla'i»uiluVttifyJfotftiniWDELai.VtrifvThNta.LD.iFT-aialii-JD).Search.i-Ldt-
17、i-J-fiinHajLUXLmdJrifani.FroWi_alodelDoiJciuviLyzi打心寸匸mplu述glyzTf-knsr-Jiibro>a際血Lhttkdlrl心Urtked?*LLWM.PiraiTiete-rPdidfri±t±rVluehr>jtSequenceAligrrnentUntitiedl.tfiriirsJiite&lhf>jtlecriplatStructuresiuwOAhputMadalSfiqucncAhtidvdl団CjoppFromTeinplilesE9NurnherofModels5Ciptim
18、izjtiDnLn-ielHigh日AckntedCutOvErhdKigsTue»DifuHid*Drklge;£y?4Q-rCysSljCCyp&fl-<y51Tl1TZy?14GKyCis-ProlintsAdditionalFtrjints-®RjpfneLoops-Tut同ParjHtlPrQopjjingFall?B-uildHoimologyModQ-口罰Ii5h5L汁:YALIc:LHDF1<;LH0P1uLOliRDFHCEKDNtND*£tdtu$et£isEkpstdTime=tdrtDateTEeru
19、itrL口丘血11QNoSuccess42.3feidtntitY.U0iDM7KJI7!::localhD5ti9943No'luCCA-Sfi47.3%汩抽現(xiàn)UEDfiSiS雋三四月口“工lacdlhoEt943NoSuccessB9hrte=UrtftiipdljgiD&4.9*.=!»:::locjlhDsU994審上dignSequence+AlignSwqufrncft由BLAST5tard-i動力學模擬1、選擇ser36-val175部分日0*INAP.rewWI麗1皿0"白gjiMINGAP&0/SER.36tEH/mFAR.G37&
20、#177;回WILE期FF0/THR39&0/ME"&EJ«PCMl莊0/MFGLN2E回沖GIY恥FT回沖EER44&VAL45&0ALA46tE底imnwTE回"GD華FF05ER49&EJaIRSO&0/CVS51空H/MFTYR52匡回"ER52FT回舛LEUS4.I.-hLL屮丨HI"f!IFGAF_P*_1ej1stssQ6dNGAPj-uIQCQfi1LHAMGAP_nwXTJGAF_m;.Mi:PJGAP_nwM.NGAPjreMINaF_new.沖NGAPjre-.wINGFWW
21、.HIU,JGAP_nw.>1.dMLPMTLCn.M5WM顯尺畠IkIH"aIaHte門MMLPMTMMLPMTMMLPMTMMLPMTMMLPMTMMLPMTMMLPMTMMLPMTMMLPMTLCR.MSMJMLLUH.M5WMLLCR.MSMJMLLCRMSWMLLCH.MLLCRMSWMlLUH.MSWMLLCR.MSMJMLLUH.M5WML|DM4MlUISCLMFLSWVESCLMFL5WVESCLMFLSWMESCLMFL5WVESCLMFL5W¥ESCLMFL5WVESCLMFL5ESCLMFLSWVESCLMFL5WVErIMFIClUFERRR
22、R&»"A432、prepareprotein(對模型進行prepare,處理蛋白并加力場)|AaQNhighr亡*l.iwtHGAF_rerfJJKAeuifrciteiriShirClRwcrt即0宅曲十*IM口LtpTMTS-'flUhFCMTdL口總±£-*tXapxviacLvltbLuo.Cd-cal-steJr&teLn.Iwiiibiy-n4iilSesLdiiep£r'T-it-ias.r;ipcr,lf'x-ipuifrt-iaxHjEkO:emo*enol£15B.ecff
23、ptor-LiEanjfiIaiterarijtis-fftsphora-jsSmallMdlecnil>EisS-raylyToalji|窩:StVl-孝審客&X:iPfllcilR.jfcIKkSiP匚!TrnllLn.1<E3TI!L-luLLXyr>iTci-n*horrEudmalhi.-pr-ia¥L-n*«HUHBcy£Lh«aLructuii.ARG-57:LE3BFHR39W.041GLN42GLY43筑gVAL45ALA4j5TR4?GLY4BPiaR50-LEU54帀i-ErtmBSterunrprVski
24、BInputPrrairJNGAP3fi-175iNGAP用BuildLOOpGTfdd卬ProkiriflieTrueHAdviariredRn>.DpLiciTTCUiE«lKilp3、minimizationoffiEJidroihiliEi£d-lJjwwG»mii*TrnxivrSvgumoathirl3»liJjSndowjj*b檢*0£打但=311說:£4站.問n円m&cdNameSiwetlDeldkRacfwii!*幗ueUCC«ll*>jWHciHCjioModsAccess+.Mmn
25、Saqyno*冶TampxiJ27*討ml卸1忖3andWffltideH:DINSiP.m用用isTempos&JEM55+:PtbbeFraoiin*EkildHurwlowMcdiiFnpvKi:JDnwdili:INGAPHChiiMnkiLRradixtiMilSuCwflEEMDL1-33Mkcn.j'mfltPM>N血JlJwESlP»PWJ95HJWECwrirdre也rrfetrdTF*too«iidii54A5T5b-eKiTSCDI£«ivwr;i+.免朋T£rrh»5J.AST5«
26、;HShiTM:Bl&e(wr;i*&I.ASTSuch£U££<&UCC4II5ThfeicMAF.iHbtUtz嚀誣E左除idanlit2i»«qu«iEvWWi5T4PP.IimMISIMPRT田wlygahiTinryGsk疋曲ctiib&o幻iE電flyuIRodEdl£ucc«ai5U£«5SS1C«55Euhkk£0LFnnn:AWMHA£00TrnruAW-NPAa5U33n&lEm"】
27、4;«MZWZMkjAwidUIMVWSIf.AruaT-df*rlaryrAnauVdyKlory2(UDn*MTMi:a>rrb£ucc«aiIriA爐*dMaliciivMrirTisBb'SnLTM£lAPj3-ipirMijAPSmanMNniSnrOil>Enangy匚hingvSorefirwi呂frcqucE3ImpSck虧出EiMcrfel圈NanbarLkxFLadiM&UK4II&1CM55SuccessAigorttimHM5C-rjidkn口占edri注PrepareProteinnIn忡El
28、郵Vru3itt|-LodeadjSuhihiaryHeiiniibtxndfhn!ZCfE5driiMm叭imfroiuihvafim-rhrt>VKh>Hpr*»i出i2frwni.d>w*FpraiisvilMi«dGfaDetail*”,屁”|汕¥申仝住忙乂,|;卜P、I二陽fE3血址jMp口H田尹IM2P-*:;蠱+QM-MM-&milMo-KuhlsAQMET圧口fMfiOEWiiw*?+OvniriljurpowS*l_JLibniryJkid-iia+口Ubr-ary口占小BoQ5郵E口儷Tida口rrsfcix0Til.
29、口曰DktiMrpEhdb*OMatfQfflrfiKuies*l_J1*jrTn«-=phsm+口RKipiorUandInKr-adanfE*SmMjOPE»-l_J»OChTralc?EQEiedradiarii:5AEn«wmdMrirrisilKn滬CdricddMErMry滬CJcweEhwDRl_滬CakdafcabriTBcripnEnirgy護MrniEUiBnETt¥*e治QhtdiphU$MIU«Bmc-wmMwrpt.rtii5Un-BHai12.1.|'1=»PPMituoiB-AI3ID9
30、CBcnlVcfwcti1-J9.I.IZ1M-海H血VCiaHJiXMtiilPitfMgu(W£=TimaIUHfMK:3ft«rriiJiTithUlW2550EiichwiTirmHOIHiSlanvVriibbTagad”亠taiirrMLciidtal=bAfirXli«i=B時處Inj帀茁看Kimr:callchQ|RaramcttirNameferaiiTieterValueInputTypedMoleculeINGAP_prep:ING/lP-MinimizafiiernAlgoirithmiSmarlIMinimizerMas璽mpt5000R
31、MSGiradienliD.lEnergyChangeD.OSaveResultsFreque-ncy10003ImplicitSolwnlMcrcH凹NonbcndLi?tRadiusDi'stancrDupmiduritDidretries14,0HElectrostEfticsSphericalCutoffI-AdvancedMinimizationConstraintsApplySHAKEConEtraintFalseINumberofPcs匸essoirsBUameForcefieldInitialPotentialEnergy(kcal/mol)PotentialEnerg
32、y(kcal/mol)VanderWaalsEnergy(kcal/mol)ElectrostaticEnergykcal/mol)InitialRMSGradient(kcal''(niolkA,FinalRMSGradient(kcaVrnolkAMinimizationCriteriaINGAPCHARMm545.S8767-2745.17219-1034.53S06-2367.49SS414.7Q785Q.09677RMS<0.1C0NJUG>Minimizationexitingwithgradienttol&rance(0.1000000)sat
33、isfiedl.4、heatingNiuinizatioiL0DynamicsQte-ilingwCooling)Q£3RarameterNameRaram&t&irValueInputTypedMoleculeINGAPifNGAPSHeatingSseps|SOODTimeStepO.QOJInitialTemperature50.0Tisrget"Femperaiiiurc-3G0.0AdjuiEtVelocityFrequency50SaveRjesultiFrequency|00D創(chuàng)ImplicitSok'entMedelDistance-
34、DependentDidectirics用NonbandListRadius14.0+EleclnostaticsSphericalCutoff日AdvancedHeatinqConstraintsApplySHAKE匚口nslnraint|thj&1HeatingSaveFfestartFileTrue1HeatinqRandomNumber£.31415931415&3141593141S9NumberofPro匚實町口itsNameForcefieldStartTime(ps)EndTime(ps)InitialPotentialEnergy(kcal/mol)
35、TotalEnergy(kcal/mol)PotentialEnergy(kcal/mol)KineticEnergy(kcal/mol)Temperature(K)VanderWaalsEnergy(kcal/mol)ElectrostaticEnergy(kcal/mol)INGACHARMm0.000010.0000-2739.314424.2269-1248.3261672.553307.79560-881.2306-2452.87736P003123023T在300左右4mmnJedEQJ5、平衡Dynairiics(XeatingorCooling)DyitimLceCEquili
36、brationj*ParameterNamePsram&t&rValueInputTypedMoleculeliNGAP-flJINGAP-EquilibrationSteps5<W0TimeStep0.002Targetlemperature300.0AdjustVelocityFrequency50SaveResultsFrequency10000ConstantPressureFalseEImplicitSolventModdDistance-DependenitDielectrics3INonbondListRadius14.00ElectrostaticsSph
37、ericalCuEoffSAdvancedDynamicsIntegratorLeapfrogVerletEquilibratianConstraintsAdplySHAKEConEtraintTrueEquilibrationSaveRestartFileTrueEquilibrationRhstartFileF:TNGAPMDDynamicslrleatingorCooling2QEquilibrationRandomINum1415fl314159314159314159NumberofProcessorsCO-1.125_=-irnnnnMonnnclnECuooooGoG0-GOQG
38、01C:=lhcelHnlpChoosePilotAxesDataRowIndexIndexNameVisibleAngleEnergyElectrostaticEnergyPotentialEnergyVanderV/aalsEnergyBondEnergyStepTimeTemperatureTotalEnergyKineticEnergyReferenceNameColcrbyDdt.赴Series-t875-1.5LILI-t250-1.375-1.625-1.75U£03040IndexPlotsel>=ctedrmsBilly6取樣(這里以10ns為例)Plarai
39、TieterNameParameterValueInputTypedMoleculeINGAP-2iINGAP'.ingl.aIipmiiiriicsi'Equi1ibration)-J1DynamiC5(Froduction);|-Production5000000TimeStepRestartFile-F:NGAP_MDDy3mic5Equilibration_2014J&1.,TargetlemperatLrm300.0TemperatureCouplingDeca,.5,0SaveResultsFrequency100&0NVTDistance-Depe
40、ndentDielectrics+NonbondListRadius14,0+Productionlyps+ImplicitSolventModelElectrostaticsSphericsICutof?AdvancedLeapfrogVerletDynamicsIntegratorProductionConstraintsApplySHAKECo-nstraintProductionRandomIMurrbw”.”True314159314159314155314159TrueProductionSaveRe-startFileNumberofPro-cesaors三.MD軌跡分析i.勢能
41、分析DataRowIndexIndexNameVisibleAngleEnergyElectrostaticEnergyPo-tenii自丨EnergyVanderV/aalsEnergyBondEnergyStepTimeTemperatureTotalEnergy_=-irnnnnMonnnclnE_(:'§'uoc二uoooo(_uo_u_|二01C:=lhcelHnlp2.RMSD分析KineticEnergy血ferenceNameAxLialyzeTr=1jectory|ParameterNameParameterValueInputMoleculeING
42、AP:NGAPPropertiesTorsionAngleProperties-RMGDRefe-rence-1ScopeMoleculeLabelRMSDto-confAtom<3blipEackb口ngAtomGrouptoFitBackboneSaveFittedTrajectoryTrue一TrajectoryFileEnergyFileFrameStartFrameStopFrame1ncr&ment3.RMSF分析(氨基酸殘基的柔性)先根據(jù)RMSD等,選取平穩(wěn)后的構(gòu)象這里假設取最后100個構(gòu)象。VisibleReferenceNTreNameTimelbLalEner
43、gyKineticEnergyC«nEorwraCanf-aiC->TitQtTia"3W.iCanf-ara1C>XritQtTi"raIIPotAntii-I.TTE*"Ia.t;£a>>oiILec;iLleirE.hceptoi-LieandIntsrticin思疋ctphoT耳吁SmjbI1Hol洋匚©lei鑫JUL-dyiti:血鈕叔唧Clui卒r-3h-a*fl«1-3FileEdit¥irvChemisbStructure15equ<«nctChartSicn
44、ptFTools則ndawHp'爭些會喚xX'+.AlignSequencetoMo1-lMi-.VBjLwe口m*=e4、*”衿話8*£昏白霸I鳳m寸5眄i.”PlBuildl-lofriDlDgQjhQNqSuccessServtrilQCdlliAEbffiJBv35jO.1215Q甌plhTF甸??IoFFPratDEDlNametfh'edDetdikElpfedTim,madek-UndoiODIdentityUQ:D0j+7j1:>dliIce曲TixaSiri-alit3dti>SaI.UpChlSU'ALUUCr-tah&
45、#187;Fln-ITrjtctoryTiatipJ.CompciDitni:Jut-ilyiis.ClientZll-rtV-Khtij3EVclx曲la廿;nohtidnohiJClioid.JlIeBond為爐£Cn&rvvtLmStatusSuccessStdrtD血StrvtrLoiZiSTtiunffl=四月9L5品Icicfilh口"朋朗HE四月9L咄申珂恤曲艸田二ffflFicIh:山E*amauLilyiuT±*«jct<UF.Ctlaallit-bVij-al*HM«nlCUcoliA電EpliustriGyr
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