How to use Autodock for docking.. Suitable for windows (not only Linux)

1. Molecular DockingMolecular Docking
using Autodock 4.2.6using Autodock 4.2.6
• Presented by/
Mariam Abdelrasoul
Teaching assistant
Medicinal Chemistry Department - Faculty of Pharmacy - Assiut University

2. AutoDock
A software for predicting the optimal bound conformations of
ligands to proteins developed by the Scripps institute of
technology
A software for docking
Why AutoDock?
Free
Credibility
Why not?
Command lines, no user friendly interface in all steps
Lengthy steps

3. A ligandA ligand TargetTarget Grid /Grid /
docking sitedocking site
Autodock Tools, ADT
….pdbqt ….pdbqt ….gpf
DockingDocking
parametersparameters
….dpf
Autodock 4
DockingDocking
….dlg
Same
folder
aS
autogri
d and
autodoc

4. Installation of AutoDock
Autodock Tools, ADT
Autodock 4
AutoDock 4.2,
Linux
AutoDock 4.2.3,
Windows / Cygwin
AutoDock 4.2.5, 4.2.6
Windows only 
Autodock vina
http://autodock.scripps.edu/

5. Steps:
1. Preparation of ligand
2. Preparation of target
3. Grid map optimization
4. Selection of docking parameters
5. Running docking
6. Analysis of results
ADT
Autodock 4

6. Ligand / Input / Open
1. Preparation of ligand
Draw and save as mol2 or pdb file
Ligand / Output ….. ligand.pdbqt

7. 2.Preparation of target
File / Open……………. XXXX.pdb
Edit / Charges / Add kollman charges
/ Compute Gasteiger
Edit / Hydrogens / Add polar
Save ………….
Edit / Delete water molecules
(β-adrenergic receptor and carazolol, 2rh1.pdb)

8. 3. Grid map optimization (2 methods)
Grid / Macromolecule / Choose…
Save as target.pdbqt
Grid / Set map type / Choose ligand .pdbqt
Grid / Grid box…… parameters
File / close saving current
Grid / Output / Save gpf …… Grid.gpf

9. 4. Selection of docking parameters
Docking / Macromolecule / Set rigid filename
Docking / Ligand / Choose
Docking / Search parameters / Genetic algorithm
Docking / Docking parameters
Docking / Output / Lamarckian…. Docking.dpf

10. 5. Running Docking
Start menu / Run ….. cmd.exe
Command lines:
cd folder name/ path
autogrid4 –p grid.gpf [-l grid.glg]
autodock4 –p dock.dpf [-l dock.dlg]

11. 6. Analysis of results
Analyse / Docking / Open …….. .dlg
Analyse / Conformations / Play….
show conformations
Analyse / Clusterings / Show
Analyse / Macromolecule / Choose

12. Thank you