AutoDock-分子對(duì)接步驟

1、Discovery studio:File -> New -> molecule window :出現(xiàn)如下窗口，將所要處理的分子 *.sdf文件拖入,Chemistry -> hydroge ns -> 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 -> hydroge ns -> add.（加上所有氫，包括質(zhì)子化的氫原子）岳 70詰甲卜 x ii J5 «3t TiiKEQHalQUu F9fZ 4>ail-d wcl E4i*. hd-Kir txhAS

2、ail J IJi I Tj laih2FraLfalMSbir-du -Chui &>i wran ' ET' Uk雷干聖空X亙紳7 *0 宜 hLow |jpPdbqt 格式準(zhǔn)備（pymol）:4M48-DAT.pdb用pymol讀入：點(diǎn)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 -> save molecular: sele - OK -重命名 ligand.pdbFile -> ope n -> Duloxet in e_3d.sdfSave > molecular : Duloxeti ne-3d.

3、pdb受體準(zhǔn)備：1. Pymol軟件：pymol打開兩個(gè)蛋白分子的pdb格式，將SERT-model疊合到4M48-DA T上，保存疊合后的SERT-model.pdb。（此步驟是重新定義SERT-model的坐標(biāo)）2. AutoDockTools: file -> ReadMolecule: SERT-moldel-align.pdbEdit -> Hydroge ns : polar Only -> OkGrid -> Macromolecule -> choose :SERT-moldel-align.保存為:SERT-moldel-align.pdbqt配

4、體準(zhǔn)備：Liga nd -> in put -> ope n : （*.pdb） liga nd.pdb | Duloxet in e-3d.pdbLigand -> Output -> Save as PDBQT: 保存為 *.PDBQT 文件。找活性位點(diǎn)，計(jì)算格點(diǎn)：Grid -> Macromolecule -> ope n : SERT_model_alig n.pdbqt彈出對(duì)話框： NO、確定、確定Liga nd -> in put -> ope n : liga nd.pdbqt 彈出對(duì)話框：確定Grid -> set map

5、types -> choose liga nd : liga ndGrid -> GridBox -> center -> center on ligand :存圖片或 output grid dimensions file | closesaving curre ntLiga nd -> in put -> ope n : Duloxeti ne_3d.pdbqt 彈出對(duì)話框：確定Grid -> Macromolecule -> choose : SERT_model_alig n 彈出對(duì)話框:Grid -> set map types

6、-> choose ligand : Duloxetine-3dGrid -> output ->save GPF :SERT-Drug.gpfRun -> AutoGridNO、確定、確定<:'-.9Xn AutoGridMacro NameHost Name:wangpplDRBmacrosWoriting DirectoryBrowseProgram PathnameParameter FilenameLog Filename:BrowseD:wang panpan svmd oc king'Aut oDock- researc hBrows

7、e|f /$aftware/AUTOdock/autogrid4 exeBrowsewangpp-IDRBNice Level20Cmd |F /software 'AtJTOdock/auiogricI4 exeD /wangpmnpan秋nv'dgkjng/AutoDock-rgse8rch/SERT-Drug gpf -ICancelLaunch提交成功，呈現(xiàn)如下對(duì)話框:生成一系列*map文件和SERT-Drug.glgDocki ng :Dock ing -> Macromolecule ->set rigid file name: SERT-moldel-

8、alig nDock ing -> Liga nd -> choose : Duloxeti ne_3d彈出對(duì)話框：AcceptDocki ng -> Output -> Ge netic Algorithm (4.2) | Lamarckian GA(4.2): SERT-Drug-dock.dpfRun -> AutoDock提交后呈現(xiàn):結(jié)果分析:An alyze -> docki ng -> ope n :*dlg (SERT-Drug-dock-GA.dlg |SERT-Drug-dock-lamarkia nGA.dlg) An alyze ->c on formatio ns > play : 可看各個(gè)構(gòu)型。(Liga nd -> in put -> ope n : liga nd.pdbqt兩個(gè)相比，可以看到哪個(gè)構(gòu)型與樣本配體結(jié)構(gòu)最相似)N Duloxetine_3dDockiBhBoard | AniMol | ToolsngppX. ng 1|CMD1 : NoneIH | <J I |l 上JO » HI 3le 3D Graphics Edi