AutoDock Vina will allow you to dock one ligand at a time into a protein/nucleic acid structure. You can select the specific region of the protein to investigate.

If you think more than one ligand binds in different binding pockets you could always do multiple docking runs each time focussing on a different region to dock into. 

If you are looking at more than one ligand binding into the same pocket then it becomes more complicated and I think you would have to make a new pdb/pdbqt file which includes the 1st docked ligand. Then run this file and try to dock in another ligand. Repeat process for even more ligands!

Its important to remember that docking will only give you a suggestion as to the answer. It will also give you lots of possible interactions, many of which are probably not relevant. Look for the lowest energy docks.

If you have the receptor/protein and the ligand you could try the experimental techniques ITC or SPR which should give you a better idea to the ratio of ligand binding to receptor.

Dear Sir,

Thanks a lot for your answer

Regards

Farideh

Hi,

As mentioned above you can dock one ligand at a time in autodock vina. For multiple ligand docking you can try iGemDock. Hope this helps.

Regards

Hi,

Thanks for your information,Could you tell me if that is a free software?

Regards

Hi,

Yes iGemDock is a free software.

Regards

Docking multiple ligand onto the pocket region of your protein need to build a database of your ligands and then dock onto protein at once using MOE or GOLD.

u can save many conformation for each ligand in a resulting database and then check the binding energy and interacting residues.

regards

For multiple ligand docking, you can also try Schrodinger's Glide.