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Graphical-AutomaticDrugDesignSystemforDocking,ScreeningandPost-AnalysisWindows‧LinuxiGEMDOCKDocumentationiGEMDOCK 2Copyright©2008DrugDesignandSystemsBiologyLaboratoryofNationalChiaoTungUniversity,Taiwan 3ContactingUserSupportIfyouhaveatechnicalproblemwithouriGEMDOCKyoucancontactourresearchgroupinTaiwan.DepartmentofBiologicalScienceandTechnology&InstituteofBioinformaticsNationalChiaoTungUniversityName:Dr.Jinn-MoonYangAddress:75PO-AiStreet,Hsinchu,Taiwan,30050,ROCOffice&Lab:308and304(Lab)inExperimentBuildingTel:886-3-5712121ext.56946Fax:886-3-5729288E-mail:moon@faculty.nctu.edu.twOrCometoourwebsite: 4CONTENTSIINTRODUCTION............................................................................................................6IIINSTALLATION..............................................................................................................81SYSTEMREQUIREMENTS...................................................................................................82INWINDOWSXP/VISTA....................................................................................................83INLINUX........................................................................................................................11IIIGETTINGSTART..........................................................................................................131OVERVIEW......................................................................................................................132BINDINGSITEPREPARATION............................................................................................153LIGANDPREPARATION....................................................................................................184RUNNINGIGEMDOCK.................................................................................................19Setupoutputpath..............................................................................................................19SetuptheGAParameters.................................................................................................19AdvanceOptions...............................................................................................................20StartDocking....................................................................................................................215POST-ANALYSISINIGEMDOCK....................................................................................23Loadingbindingsite.........................................................................................................23Loadingdockedposes.......................................................................................................24Generatinginteractionprofile..........................................................................................24Clusterbasedanalysis......................................................................................................26Savepost-analysisdata....................................................................................................27TheoutputdataofiGEMDOCK.......................................................................................28Importingyourdatatoexcelforadvancedstudy.............................................................28IVADVANCEDFEATURES..............................................................................................30BINDINGSITEPREPARATION..................................................................................................301.iGEMDOCKcannothelpmetopreparemybindingsitewhenmyproteinfileisnotoriginalPDBfileorhasnoligand.HowcanIpreparemybindingsiteunderthese 5situations?.........................................................................................................................302.Myproteintargetneedstoconsiderthecofactorormetalionindockingcalculation.CaniGEMDOCKrecognizethesenon-aminoacidmoleculesinthedockingcalculation?...................................................................................................................................34LIGANDLIBRARYPREPARATION.............................................................................................353.IwanttopreparetheboundedligandfromPDB.HowcanImakeit?.....................354.Iwanttoconstructligands/ligandlibraryforscreening.Isthereanyexample?.....43SCORINGFUNCTIONOFIGEMDOCK....................................................................................545.Iwanttore-scoremyeverpredictedposesagainstaproteintarget.Howtodoit?.546.WhatisthemeaningofeachterminGEMDOCKinteractionprofile?....................577.WhatisthepharmacologicalconsensusmethodmentionedinProteins:Structure,Function,andBioinformatics,vol.59,pp.205-220,2005?Howtousethesetermsinmyscreening?.........................................................................................................................59COMMANDMODEOFIGEMDOCK........................................................................