Autok-分子對接步驟

1、Discoverystudio:File-New-moleculewindow:出現(xiàn)如下窗口，將所要處理的分子*.sdf文件拖入,Chemistry-hydrogens-dele去掉所有氫，選中質(zhì)子化的氮原子選中質(zhì)子化的氮原子，Chemistry-charge:+1.Chemistry-hydrogens-add.（加上所有氫，包括質(zhì)子化的氫原子）a12Pdbqt格式準備（pymol）:4M48-DAT.pdb用pymol讀入：點右下方S鍵，在左上方顯示序列，選中21B,右側(cè)顯示有sele后，file-savemolecular:sele-OK-重命名ligand.pdbFile-open-D

2、uloxetine_3d.sdfSavemolecular:Duloxetine-3d.pdb受體準備：1. Pymol軟件：pymol打開兩個蛋白分子的pdb格式，將SERT-model疊合至U4M48-DAT上，保存疊合后的SERT-model.pdb。（此步驟是重新定義SERT-model的坐標）2. AutoDockTools:file-ReadMolecule:SERT-moldel-align.pdbEdit-Hydrogens:polarOnly-OkGrid-Macromolecule-choose:SERT-moldel-align.保存為：SERT-moldel-align

3、.pdbqt配體準備：Ligand-input-open:（*.pdb）ligand.pdb|Duloxetine-3d.pdbLigand-Output-SaveasPDBQT:保存為*.PDBQT文件。找活性位點，計算格點：Grid-Macromolecule-open:SERT_model_align.pdbqt彈出對話框：NO、確定、確定Ligand-input-open:ligand.pdbqt彈出對話框：確定Grid-setmaptypes-chooseligand:ligandGrid-GridBox-center-centeronligand:存圖片或outputgriddim

4、ensionsfile|closesavingcurrentLigand-input-open:Duloxetine_3d.pdbqt彈出對話框：確定Grid-Macromolecule-choose:SERT_model_align彈出對話框：NO、確定、確定Grid-setmaptypes-chooseligand:Duloxetine-3dGrid-output-saveGPF:SERT-Drug.gpfRun-AutoGridMacroNameHostName:nAutoGrrdwangpplDRBmacroswangpp-IDRB,/FkingDirectoryProgramPath

5、nameParameterFilenameLogFilename:D:wangpanpansvmdockingAutoDock-research|f/$aftware/AUTOdock/autogrid4exeBrowseBrowseBrowseBrowseMacromolecule-setrigidfilename:SERT-moldel-alignDocking-Ligand-choose:Duloxetine_3d彈出對話框：AcceptDocking-Output-GeneticAlgorithm(4.2)|LamarckianGA(4.2):SERT-Drug-dock.dpfRun

6、-AutoDock7RunAutoDoc舉1MacroNamewangpp-IDRBmacrosHostName:目ngpp-IDRSWorkingDirectoryD:wangpanpansvmdockingAut口Duek-researchBrowseProgramPathname:|F:ware/AUTQdock/autoJockJ.BrowseParameterFilename:10:/wangpanpansvmjdocking/AutoDock-research/SERT-Drug-ddck.dpfBrowseLogFilename：0/wangpanpansvm/docking/A

7、utoDock-research/3ERT*Drug-dockdig日rows。AddOptionalFlagsCYes荷NoNiceLevel:20Cmd:|F/softwareWUTOdck/autodocking-open:*dlg(SERT-Drug-dock-GA.dlg|SERT-Drug-dock-lamarkianGA.dlg)Analyze-conformationsplay:可看各個構(gòu)型。(Ligand-input-open:ligand.pdbqt兩個相比，可以看到哪個構(gòu)型與樣本配體結(jié)構(gòu)最相Ie3DGraphicsEditSelectDisplayColorComputeHydrogenBond