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AutoDock_doc_japanese_ver.1.0

skume
April 19, 2023

 AutoDock_doc_japanese_ver.1.0

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。

skume

April 19, 2023
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  1. 1
    120704 ver. 1.0
    Presented by Satoshi Kume, Osaka Pref. Univ.
    How to use AutoDock 4.2 on Mac
    1. Auto Dock (http://autodock.scripps.edu/)ͱ MGL Tools (http://mgltools.scripps.edu/)Λμ
    ΢ϯϩʔυ͢Δɻ
    2. MGL Tools ͷ AutoDock Tools Λىಈ͢Δɻ
    3. Protein Data Bank(http://www.rcsb.org/pdb/home/home.do)ΑΓ PBD ϑΝΠϧΛऔಘ͢Δɻ
    3. Protein ͱ Ligand ͷ PDB ϑΝΠϧ͔Β PDBQT ΁ม׵͢Δɻ
    PDBQT ϑΝΠϧ͸ɺݪࢠిՙͱ Torsion ͷఆٛΛ෇͚Ճ͑ͨ PDB ϑΝΠϧͰ͋Δɻ
    a. Process for Protein
    File → 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 → Save
    PDBQT)
    Edit → Delete → All molecules
    b. Process for Ligand
    Ligand → input → open Ligand PDB File
    Ligand → Torsion Tree → Direct Root
    Ligand → Torsion Tree → Choose Torsions → Done
    Ligand → Output → save as PDBQT
    Edit → Delete → All molecules
    4. Protein ͷ flexible residues Λઃఆ͢Δɻ
    Flexible Residues → Input → Open PDBQT file
    flexible ʹ͍ͨ͠ Amino acid residues ͷ Sel.(select)Λબ୒͢Δ(less than 32 residues)ɻ
    flexible Residues → Choose Torsions in Currently Selected → Residues → OK
    flexible Residues → Output → Save Flexible PDBQT or Save Rigid PDBQT
    Edit → Delete → All molecules

    View Slide

  2. 2
    5. GridBox Λઃఆ͢Δɻ
    Grid → Micromolecules → Open PBDQT file
    Grid → Set Map Types → Open ligand PDBQT file
    Grid → Grid Box → Grid Box ͷઃఆ → File → close saving current
    Grid → output → Save GPF
    6. Run AUTOgrid
    ͢΂ͯಉ͡ File ಺Ͱߦ͏ɻ
    RUN → AUTOgrid4
    Program Pathname → universal darwin10 ͷ AUTOgrid4 Λબ୒
    Parameter Filename → gpf file
    Log Filename → glg file
    λʔϛφϧΛىಈ → bash Λىಈ͢Δ
    PDBQT ͷ͋Δ File ·ͰҠಈͯ͠ɺCMD ίʔυΛష෇͚ɺEnter
    Map file ͕Ͱ͖Δɻ
    Edit → Delete → All molecules
    7. Docking ύϥϝʔλΛઃఆ͢Δɻ
    Docking → Macromolecules → Set Rigid Filename → PDBQT File of Protein
    Docking → Ligand → Open PDBQT File of ligand → Accept
    Docking → Search Parameters → Genetical Algoritm Parameters → Number of GA Runs ≥ 200,
    Maximum Number of generation: 270000 → Accept
    Docking → Docking Parameters → Accept
    Docking → Output → Lamarckian GA
    8. RUN AUTODOCK4
    RUN → RUN AUTODOCK4
    Program Pathname → universal darwin10 ͷ AUTODOCK4 Λબ୒
    Parameter Filename → dpf file
    Log Filename → dlg file
    λʔϛφϧΛىಈ → bash Λىಈ͢Δ
    PDBQT ͷ͋Δ File ·ͰҠಈͯ͠ɺCMD ίʔυΛష෇͚ɺEnter
    ΞΫςΟϏςΟϞχλͰ Autodock ͷಈ࡞Λ֬ೝɻ
    MGL Toolsɺٴͼ X11 ͸ফͯ͠΋େৎ෉ɻ

    View Slide

  3. 3
    9. Docking Data Analysis
    AutoDock Tools) Analyze → Docking → Open DLG file
    Open PDBQT file of Protein
    Analyze → Clustering → Show
    (Xterm → cd file → less DLG file → /Rank → /number / → control + Z)
    10. Pymol Ͱͷ Docking ϑΝΠϧͷ࡞੒ ~ dlg ϑΝΠϧΛ pdb ϑΝΠϧ΁ม׵ ~
    Terminal) cd docking file
    Terminal) grep '^DOCKED' ???.dlg | cut -c9- > ???.pdbqt
    Terminal) cut -c-66 ???.pdbqt > ???.pdb
    Terminal) less ???.dlg
    Pymol) File → Open PDB file of Ligand Docking
    Pymol) File → Open PDB file of Protein
    ௥ه
    11. ϦΨϯυ pdb ϑΝΠϧͷ࡞੡
    ᾇChemskech software ͰϦΨϯυͷԽֶߏ଄ࣜΛ࡞੡͢Δɻ
    Tools ˠ 3D ….
    File ˠ Export ˠ save .mol file
    Open .mol file by Chimera ˠ save as a pdb file
    ᾈ Pubchem ͷ SMILE ͔Β PDB file ͷ࡞੡
    Pubchem ͰϦΨϯυͷ SMILE Λίϐʔͯ͠ɺCORINA demo ʹ Submit ͢Δɻ
    CORINA (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 ʹม׵͢Δɻ
    12. Pubchem ͷ SMILE ͔Β logP ܭࢉ
    ALOGPS ʹϦΨϯυͷ SMILE Λϖʔετͯ͠ɺSubmit ͢ΔɻlogP ΍ pKa ͳͲ͕ܭࢉ͞ΕΔɻ
    http://www.vcclab.org/lab/alogps/

    View Slide