This is a manual of AutoDock & AutoDockTools in Japanese. Autodock is a molecular docking simulation software.
AutoDock & AutoDockToolsに関する日本語マニュアルです。Autodockは、主にタンパク質-低分子化合物の複合体予測を行うソフトウェアです。
1120704 ver. 1.0Presented by Satoshi Kume, Osaka Pref. Univ.How to use AutoDock 4.2 on Mac1. Auto Dock (http://autodock.scripps.edu/)ͱ MGL Tools (http://mgltools.scripps.edu/)Λμϯϩʔυ͢Δɻ2. MGL Tools ͷ AutoDock Tools Λىಈ͢Δɻ3. Protein Data Bank(http://www.rcsb.org/pdb/home/home.do)ΑΓ PBD ϑΝΠϧΛऔಘ͢Δɻ3. Protein ͱ Ligand ͷ PDB ϑΝΠϧ͔Β PDBQT ม͢Δɻ PDBQT ϑΝΠϧɺݪࢠిՙͱ Torsion ͷఆٛΛ͚Ճ͑ͨ PDB ϑΝΠϧͰ͋Δɻa. Process for ProteinFile → Read Molecule → Open PDB file (Check Ribon.)Edit → Hydrogens → add → Polar only → OK.Edit → Charges → Compute Gasteiger → OK(Edit → Hydrogens → Merge Non-Polar)(Edit → Atoms → Assign AD4 type)File → save → Write PDBQT (or Grid → Macromolecule → Choose ಉ͡ PDB file → SavePDBQT)Edit → Delete → All moleculesb. Process for LigandLigand → input → open Ligand PDB FileLigand → Torsion Tree → Direct RootLigand → Torsion Tree → Choose Torsions → DoneLigand → Output → save as PDBQTEdit → Delete → All molecules4. Protein ͷ flexible residues Λઃఆ͢ΔɻFlexible Residues → Input → Open PDBQT fileflexible ʹ͍ͨ͠ Amino acid residues ͷ Sel.(select)Λબ͢Δ(less than 32 residues)ɻflexible Residues → Choose Torsions in Currently Selected → Residues → OKflexible Residues → Output → Save Flexible PDBQT or Save Rigid PDBQTEdit → Delete → All molecules
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25. GridBox Λઃఆ͢ΔɻGrid → Micromolecules → Open PBDQT fileGrid → Set Map Types → Open ligand PDBQT fileGrid → Grid Box → Grid Box ͷઃఆ → File → close saving currentGrid → output → Save GPF6. Run AUTOgridͯ͢ಉ͡ File Ͱߦ͏ɻRUN → AUTOgrid4Program Pathname → universal darwin10 ͷ AUTOgrid4 ΛબParameter Filename → gpf fileLog Filename → glg fileλʔϛφϧΛىಈ → bash Λىಈ͢ΔPDBQT ͷ͋Δ File ·ͰҠಈͯ͠ɺCMD ίʔυΛష͚ɺEnterMap file ͕Ͱ͖ΔɻEdit → Delete → All molecules7. Docking ύϥϝʔλΛઃఆ͢ΔɻDocking → Macromolecules → Set Rigid Filename → PDBQT File of ProteinDocking → Ligand → Open PDBQT File of ligand → AcceptDocking → Search Parameters → Genetical Algoritm Parameters → Number of GA Runs ≥ 200,Maximum Number of generation: 270000 → AcceptDocking → Docking Parameters → AcceptDocking → Output → Lamarckian GA8. RUN AUTODOCK4RUN → RUN AUTODOCK4Program Pathname → universal darwin10 ͷ AUTODOCK4 ΛબParameter Filename → dpf fileLog Filename → dlg fileλʔϛφϧΛىಈ → bash Λىಈ͢ΔPDBQT ͷ͋Δ File ·ͰҠಈͯ͠ɺCMD ίʔυΛష͚ɺEnterΞΫςΟϏςΟϞχλͰ Autodock ͷಈ࡞Λ֬ೝɻMGL Toolsɺٴͼ X11 ফͯ͠େৎɻ
39. Docking Data AnalysisAutoDock Tools) Analyze → Docking → Open DLG fileOpen PDBQT file of ProteinAnalyze → Clustering → Show(Xterm → cd file → less DLG file → /Rank → /number / → control + Z)10. Pymol Ͱͷ Docking ϑΝΠϧͷ࡞ ~ dlg ϑΝΠϧΛ pdb ϑΝΠϧม ~Terminal) cd docking fileTerminal) grep '^DOCKED' ???.dlg | cut -c9- > ???.pdbqtTerminal) cut -c-66 ???.pdbqt > ???.pdbTerminal) less ???.dlgPymol) File → Open PDB file of Ligand DockingPymol) File → Open PDB file of Proteinه11. ϦΨϯυ pdb ϑΝΠϧͷ࡞ᾇChemskech software ͰϦΨϯυͷԽֶߏࣜΛ࡞͢Δɻ Tools ˠ 3D …. File ˠ Export ˠ save .mol file Open .mol file by Chimera ˠ save as a pdb fileᾈ Pubchem ͷ SMILE ͔Β PDB file ͷ࡞Pubchem ͰϦΨϯυͷ SMILE Λίϐʔͯ͠ɺCORINA demo ʹ Submit ͢ΔɻCORINA (http://www.molecular-networks.com/online_demos/corina_demo)ᾉ Pubchem ͷ sdf file ͔Β PDB file ͷ࡞ϦΨϯυͷ sdf file Λμϯϩʔυͯ͠ɺChimera Ͱ pdb file ʹม͢Δɻ12. Pubchem ͷ SMILE ͔Β logP ܭࢉALOGPS ʹϦΨϯυͷ SMILE Λϖʔετͯ͠ɺSubmit ͢ΔɻlogP pKa ͳͲ͕ܭࢉ͞ΕΔɻhttp://www.vcclab.org/lab/alogps/