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。

Transcript

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