Molecular docking software Autodock 4.2.6 is presented. It is free and credible for predicting optimal bound conformations of ligands to proteins. The steps for using Autodock include: (1) preparing the ligand and target protein, (2) optimizing a grid map, (3) selecting docking parameters, (4) running the docking simulation, and (5) analyzing the results. Autodock Tools (ADT) is used for preparation of files in .pdbqt format before docking with Autodock 4.

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