Sybyl對(duì)接教程

1、Sybyl對(duì)接教程1先建立存放需要對(duì)接的蛋白和小分子的文件夾3D QSAR5J5S2015/12/9 16:17文碾books2015/12/29 10:50CADD文本町順教程2015/12/29 15:53DATA2014/12/1 20:26decking2Q1S/2/23 21;11docking sybyl2016/2/26 18:26Fave riteVideo2015/12/24 17:02文磁¥ ia3016/2/24 9:361 JMC Article?2O1&/2/22 14£5文除我建立的dock in g_sybyl文件夾。文件夾里面放有靶點(diǎn)

2、蛋白和需要對(duì)接的小分子，如下圖輕稱攜改曰陰TH>大丿4rsfdocktmpdir2016/2/23 20.2&文彳快1 dlg.pdb501672/22 20:12Accelry Discove.,.675 KB AMD.mol22016/2/23 20:31Accelrys Discover,6 KBNUl2016/2/23 20:33文件0 KB設(shè)置對(duì)接文件夾路徑：Optio ns set宀DefaultDirectoryAnalyze Results.Analyze Combinatcrial Resiilts.找到docking_sybyl文件夾，點(diǎn)擊OK下面開始對(duì)接：A

3、pplicationDocking Suite f Docking LigandsCompute| Applications giopolynner UNITYOption? HelpLigand Preparation1 H楚/ .上魚FDock LigandsDocking SuiteSimilarity Suite*Align Compounds>Pharmacophore- Alignment RACHEL,.FlexE - Prepare PDB Files.QSAR ToolsTcppmr CqMFACScore Subse-t.Library Design進(jìn)入Docking

4、界面。Q DockingDefine.Dockinig Mode: SurELex-Dock (SFXC)JobnameDockin.cRun.jD01Abot .Cancel點(diǎn)擊 define,進(jìn)入 Surflex-Dock 界面。1 I 匚ombinatori al:CombiDock1 1 Cflnxtr ftantsLu. ； Dtfine ，F(xiàn)il mnam e:SurfleiDock.-Opti dock.Runting-.:J Perform CScore CalculatiiciiiECScore Letails.Frep&re導(dǎo)入蛋白結(jié)構(gòu)，點(diǎn)擊紅圈中下拉框進(jìn)入dock

5、ing_sybyl文件夾。D'Lrcstsry；i ； /d« dIq平 Q 諒 * £Bohn&rks .>|» Uircct-Mry JsviitioiLStlecticz.IJCWD：PairntF«DMe M edifiedIS HOME；dlg pdb201bJ/22$TA_DEMOiFlit( OE |Files gf Trpe= |FJB JIU w, jdb jdb_ Z *. pip ;i x eti. 3 忙 es；L ex 事 cr：l pib*“ 昶 遲 <tn X * | CTi-celHelp選擇3

6、dlg.pdb 點(diǎn)擊OK這樣蛋白已經(jīng)導(dǎo)入sybyl窗口Fr.RuJKFri7tAi"n SlrrrtrTf-杖FUli-口曠冷3町匕r-SFrf-parpK &EL d.TL* E341.ji<ar-/H). 50-3oUAL'UaTrot till cl:SriC P 訂Q 341;訛LU *=O-D ttS4?f u?fii0 SO BloM U)Mvl Aitdwhcld. i 口Ant cm-tk ticLi .-uidE; Surflcx-Ooflt - Define SFXC Fik接下來(lái)對(duì)蛋白點(diǎn)擊 Prepare。Prepare Protein S

7、trurtur?Mol Area.M ole coleml: 3dlgEk tjrac t L丄 gfindL Sube true tur e e_ . .Remove SuTiEtructureE.-Analyze： Selected Structure點(diǎn)擊 Extract Ligand Substructures （提取小配體）。Llh«i-i/FHOIl：SD2!01/ILLZI1999陽(yáng)3W»/PMJ30La/RMFPMJSOC1/IU5Wi岸0 Setect SubsOrucliJif sIJ Hidfc asL亡匚“dLl="e1 SelectedSi

8、ibstrujclujcs.fliteirA/31-SL001* IA/2K1003 A/JI0R10MA/WOIU05X 帶2QGE船用朋nrwa選擇小配體GWE999點(diǎn)擊OK點(diǎn)擊RemoveSubstructures（刪去無(wú)關(guān)的水分子和離子）點(diǎn)擊OK到此蛋白已經(jīng)準(zhǔn)備好O Prepare Protein Structure叵R亡n剖n亡Att-msSAtomsBackboneS i >1Add HydrogensSet Frotonaticm TypeType KtFi x 5i dechiin Anti dtsSi d«ch&m B-umps點(diǎn)擊 Return。0s

9、h«w'0Show'oDShu賈0Show郴皀wi du*j*E#盟色兮i du&s#Hes;i dues和亡si dues糅弓1si du«sor點(diǎn)擊OKShewShow*點(diǎn)擊Gen erate，產(chǎn)生活性位點(diǎn)即產(chǎn)生 protomol,3dlg_H-L-0.50-0-protomol.mol2點(diǎn)擊0KDockingXBoffking : 5«rfltK_Doak CSFXlPilwian: 3也lK-IX! 50-0 OptiBockCombiDockCoabiTiAtoriel；FileQOpen曲旦 SpreadsheetFrpar*.

10、-Surflx-Dock.Opti dock .Euntirr.e ./ frforn 匚Score CalculiticinmCSccire Jet ails.Job Option呂Dock! ngKinAbout.Cpti otis在Ligand source下拉框中有常見的小分子格式可以選擇，看你要對(duì)接的小分子是什么格式就選什么格式。我的是mol2格式就選擇mol2 file點(diǎn)擊紅圈中下拉框，選擇需要對(duì)接的小分子選擇AMD.mol2點(diǎn)擊OKProc根據(jù)你的電腦的核數(shù)來(lái)確定，我的是兩核，填2。四核填4Job name可以根據(jù)習(xí)慣自己命名。點(diǎn)擊0K開始對(duì)接 等待。對(duì)接完后出現(xiàn)Result B

11、rowser界面。Reult-s BrokerJobrame' Va'CkingRunlLi規(guī)and Index: n1 Mo Li sled:- 丿F1|JZOO E>MiirL HHaI1*、L(>1 iVi ew: _W jConstr *ints.Tot； 1f0£； (JSal； 0Wrk； Ct叵IULskJ回Visuali zati on.F ule d Li arids.AVfeCloseView 選擇 Dock in gR un 1_site.mol2點(diǎn)擊小分子AMD出現(xiàn)結(jié)合模式。點(diǎn)擊 save result0 Save Resultsf

12、floda；SelectedCriteri a!Tot al_ScoieOrd*r.QaicmdisTEave ModeFirst HFirst N fiesceiLttzn Total_ScoareNwlar of F cises par Li gmdD 3trip Fcse Number From MoleciiLe NameAppF frs& ColumnOutput Per*atsS£) FlIaMui £1. - B ol2J SpreadsheetMDS 3 SUT FxleWtppt Irstix ftesultsJOl設(shè)置如下：每個(gè)配體保留3個(gè)構(gòu)象點(diǎn)擊OK顯示小分子前3個(gè)構(gòu)象選擇第一行，顯示藍(lán)色，點(diǎn)擊 3D。選擇 M2:3dlg，點(diǎn)擊 Specify點(diǎn)擊BD Vie.*er Preferen匚芒5Row 0 i spl «ty蚌plyCancelR«nderingLln«sTM Di spl ayPolar OnlyCol er(?R£ENVLabelsReset to DefaultsRe £«r«nc電 Di splay設(shè)置顯示的顏色風(fēng)格等。還可以保存純蛋白和對(duì)接后的小分子，用來(lái)做分子動(dòng)力學(xué)7 尺亡弓 u Its Browser:Cons<.r tin