DS2.5使用教程

1、DS2. 5使用教程DS2.5使用教程小分子1 .畫圖:小分子結(jié)構(gòu)用chemidraw畫好。 另存為mol格式，文件名不支持中文。 Check快捷鍵為V2 .啟動DS2.5打開小分子File-*open注意:Structure Sequence Chart 女 ript， Windov/ Help回尋多余 3 a： ：o： ；ii； a : a k專Ehp5ed Tim<»DateOutput location Server LocationDeta«hServer: httpc/locolhostG3«Minimization搜 Minimization單

2、擊Tools中的Minimization,屏幕左側(cè)，Tools欄展開Simulate structures：Forcefield：選 CHARMm單擊 Apply Forcefield單擊展開區(qū)最下方Minimizationuiscovery btuaio Client 2.3£勒學(xué)©卷X 乂電電Scripts Window Help，MenwProtocolsAll。«=> 十，Tools.ecule ConformationsForcefieldForcefield： CMARWmPartied Charge: HApply Foret fi «

3、;ldCl1-(2,4-Difneth- BN。1 1More.Fnrrpfi p!Heli) JToolsCale EnergyMinimization 單擊Minimi z&tion/ Quick ProtocolsMinim tionAle Edit View Chemistry Structure Sequencprt J iTiinimi zationV »eValidate Protein Structure Vi suali ze Receptor-Li gaixd.Fil«s ToolsCmstomaz< Phtrm*cophor< F.

4、 Define and. Edit Binding Site E4i t md Cluster Ph<rmaco.H oleculeresEdi t Xray StructureN<nd L.b.l 3D_Str.Place and Refine X-ray Li.Prateixi Reports sd Utxli.Search Small Molecule Coit.Search Side-Chain Rot MiersSimulate StructuresForcefield St&txis單擊1- (2 4-Dir* thylpheziyl)pip«r az

5、i Simulate Stru / Tbolsbrmation Search andIndexNameTaggedAtom W Bond JIndexNameTagged1 11- 4-Dimth-1回N。MoleculeAtom Bond J Chain J Residua J4.準(zhǔn)備搜 prepare單擊protocols下的prepare Ligands屏幕左側(cè)展開雙擊屏幕左側(cè)展開區(qū)prepare Ligands屏幕右下角出現(xiàn)prepare Ligands的相關(guān)表5.Run(F5)job提示運行結(jié)果雙擊查報告Structure Sequence Chat： Scripts Window

6、Helpjreparelean Protein,Srri3ll Molecules reMtionejtare Ug3ndsfrotocok/ Di3vcrySnd, ，GeneralLepore ligandsProteinSub.Effici. lar R.心# - Volcolc YtxdORk姨+3 4 X互：M&' A® &團上公6 f令cPDewilsElapsed Time Start Date Output Location ServerLi 鴕業(yè) x 14Parameter NameParameter Value> Input Liga

7、ndsl-(2.4-Dimethylpheny1)piperazire:Vi5ibleDuplicate StfucwresRemo'eChange IcnizlianTrue? Generate TautomercTrueGenerate IsomersTrue> Lipinski FilterFakeGenerate 3DTrueAarollel Proce55ingFalse> AdvancedServer: hrtp%/od卜05t9蛋白質(zhì)1 .蛋白質(zhì)從 /pdb 下載,或在 DS 中用 open URL功能輸入protein I

8、D號2 .打開（同小分子）3 .去水：選中左任務(wù)欄中的water, Deleteicripts Win do*/ Help（V中宓分n:二耳；n溫、a鼠?Ylindov I 4qr v - Hol acul Winds X<qrv蹌 ProtcinSequcncci A B 1al.«a Dejetef B一、Water-Helatm, Protein Groups<NameTaggedVisibleVisibility Locked CaIculate Charges4orv口附"JYc 二匚JBo=m' Ai "no人或Khain/V-Pv

9、o t。yQQC.QA_/ Aton_/ Chain_y_ Eq二i,由ia片0nL/ Gtf0W>/4力口 H：點 chemistry 到 Hydrogens 至！J H Addy Structure Sequence Chart Script，Window HelpI regent nent d ridixdlion eoehemirtry roe八 Atom:al Templates. daton Staterulate Basic Propertiescent Properties.ph«r»xer*sat5H Add，Add 七 1”Add Chiral國l

10、 HideH ShowLDelete-YuxyioR6次： X/&、A©取e 3 5,胃令:y G®BJ HetatmV 勿 Protein Group:IndexNamel<jrvTagged知VisibleVisibility Locked Calculate ChargesWleEe 八匚11 八 kmoki七han八 PrSsTSysnc 八 MicvaAcd/l N”Chan八 Rx,ds】oaa/.Gre/4 posM： 1 |2_4-0<»:071 po5es- l-(2.4-0:00:2828 po，。，： l-(2_4Star

11、t DateDetaJsElapsed TimeOutput Lccaiior Server Location用六二月 27 20尸 C:U的式FCXSQu hffpE/1ocdhC5t:9942* ZLB 27 20QU5ecAKXPc httpW/locdhostWS HA 二月 27 203 C:UcfirtfCXDc http WdhoCg425 .準(zhǔn)備搜prepare命令，單擊Protocols中的prepare protein命令區(qū)展開，雙擊prepare protein,單擊Run (F5),右下角Job區(qū)顯示進程，sucess后可雙擊看結(jié)果rcup%IndexNameViabl

12、e' 皿cull八Start DatePae涌奶。Input Protei83d LoopsProtcnaeeOutput location Server IR55 二月 2S 09：.： GU$ersFCXDd hupS/1； 因六二月 27 2X GUcersFCXDc httpii次 司六二月27 20X 6。掠5火由04府附向 冏六二月 27 20: C'Ue'FCX屈 httpsvTIiStep U5： 4qrv 000:58' 4 poscc: l-)：2.4-( 0:00:07 1 poses: 1-(2.4.1000:28 28 ps= l-(2

13、_4 0:00:49Details Eld|IntfirctioncParameter Value4qrvqrvTrueTrueViiibil<y /ted Cdculate Charges f M。 I八"Advancedted Substructure ird Effidency ecular Proper匕“RTS idsClean Protein “ Analyze Small Molecul“ PreparationPrepare Ligand。 Protocol Discovery Studio General Purpose Prepare Ligands Pre

14、pare ProtebServer: http5：771ocolho«:96.定義活性位點(1)選中配體小分子(如果有)(2)搜define命令(3) Tools 中單擊 define and edit binding site 下面的 define spherefrom selectionI 2.5rh”ml%Indexlagged，憶Prepare ?r«teio XParameter NameParameter ValueMeruTools；Prcxen Reports and UnitiesBuild and Edit Nucleic Acid【，Analyze B

15、ndiKg Site Anolyxe Docket Proteinsw 卜 FIp!.c41.八AaSeAcLdJNameqqrvvisibleWTcj "aqcoIk IdtgstiOL 二SelectedVtsuafze Re<ept/ llgand Inter(jpns , and Edit Binding S%。 fajj Sequencein- y "ProteirrCfObpsJ 5BD.Sito.Sphor0Z SeD.RrceptorVi5iEilrty Locked Caleulate Charge!女ep 5/5: 4qrv 0:0844 pow：

16、 1-(2.4-10:0007SE 二月 28 C:User5FCXDc https:/1 彳六 二月 27 20:5 CAU3eF66c bttpW/l51 8”。： 1-(2 4-(0:00:23.豆六二月 27 20乂 C:Uwr5VCXDc https:/；1ZBpooev 1<2j4(HXM9六 二月 27 20:3 C;U”c3Dc 卜ttpWAOutput Locaticn ServerDetailsElapsed Time Start DateInput Protein Build Loops Protorjte Advanced4qrv:4qv TrueTrueServ

17、er; httpsi/Aocolhs£g7 .刪除活性位點原有的配體小分子否則無法對接8 .對接搜cdocker命令點 Protocols 中 Receptor-Ligand Interactions 下面的 Dock Ligands (CDOCKER) 展開左側(cè)欄 雙擊 Protocols 中的 Dock Ligands (CDOCKER)右下側(cè)表中 Input Receptor：選 proteinInput Liands：選小分子Input site sphere 一定要選上9.Run> C ient 2.5;try Structure SequenceSwipes Win

18、.ow Hd|/匕壯、wrfS5cq，Q 端Ker公, ProtocchI“ Discovery Studio Receptor bgand ijrections1-(2. 4徇樂b1719k1皿加rerodae - Molecule YioxUv jDock ligands (CDOCKER)Interartons >d feses ding Enorgix :ore iution / yj 力 Protein Groiip， 7 SBD.Site.Sphere7 SBO.ReceptorCMCSS)IndexViableVisibility locked Calculate Charg*?口 b。ET.miKDCCKIElapsed rimeseen Dateit location ServerFrepire Frveia Doc>(C033KJX) XParameterParameter Value。po，c:, Step 5/5c 4qrv4 po2”： 12_41 po5ey 1X2L4-28 poses： l-(2.40:00:030:08:040:00970崛8 049