Autodock: Potein-ligand binding tool

AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use. AutoDock Vina has been designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The Scripps Research Institute. Vina uses the PDBQT molecular structure file format used by AutoDock. PDBQT files can be generated (interactively or in batch mode) and viewed using MGLTools. The structures of the molecules being docked and the specification of the search space including the binding site is required. The summary automatically remains in sync with the possible usage scenarios.

How to use AutoDock ?

The receptor and ligand are required in PDBQT format which is obtained

by following the given procedure :

1. File     Read Molecule (Select Receptor)

                            2. Edit    Hydrogen’s    Add      All     Hydrogen    OK

3. Color    By Atom Type    All geometries     Ok

4. Select     Select from String    Add      Dismiss

5. Edit      Delete     Delete Atom set      Continue

6. Edit     Hydrogen’s     Add Polar only      OK

7. File     Save as    Write PDB       OK

8. Ligand    Input      open (select ligand)        OK

9. Ligand    Torsion tree    Detect Root

10. Ligand  Torsion Tree     Show Root Expansion

11. Ligand  Torsion Tree       Choose Root         Done

12. Ligand  Set number of Torsions (enter6)          Dismiss

13. Ligand  Output      Save as PDBQT     Save

       14. Grid      Macromolecule      Choose       OK        Save (as PDBQT)

           15. Grid      Grid Box (Center on macromolecule)      File                  Close Saving Current

How to run AutoDock Vina ?

In order to run Auto dock vina, the following command prompt is to be used:

vina.exe --receptor name.pdbqt --ligand name.pdbqt --center_x value --center_y value --center_z value --size_x value --size_y value --size_z value --out filename.pdbqt  --log filename.txt

At the end of the run, log and output files are obtained. The log file contains the energy values and rmsd values. The output files contains the docked molecule which can be visualized using pymol.

For further help go to this link :

autodock.scripps.edu/.../tutorial

and to download the software link is provided to the right side of page, in bioinformatics software section.