Hi,

AutoDock Vina:

http://vina.scripps.edu/

Or, try several docking servers:

http://www.swissdock.ch/

http://blaster.docking.org/

http://dinc.kavrakilab.org/

http://bioserv.rpbs.univ-paris-diderot.fr/services/MTiOpenScreen/

You can also check

Article Software for Molecular Docking: A review

Article Can we trust docking results? Evaluation of seven commonly u...

https://www.researchgate.net/post/Best_docking_tools10

Hi,

AutoDock Vina:

http://vina.scripps.edu/

Or, try several docking servers:

http://www.swissdock.ch/

http://blaster.docking.org/

http://dinc.kavrakilab.org/

http://bioserv.rpbs.univ-paris-diderot.fr/services/MTiOpenScreen/

You can also check

Article Software for Molecular Docking: A review

Article Can we trust docking results? Evaluation of seven commonly u...

https://www.researchgate.net/post/Best_docking_tools10

Hi Mostafa

AutoDock is the highly cited freeware docking software, for small molecules having few torsion angles (high accuracy upto 7, but can be used for docking of molecules having torsion angles 32).

As mentioned by Snijesh, there are many softwares but choose the one which can replicate the docking poses of your control or known molecules. That will give you an edge over the others.

For macromolecular docking or protein-protein or protein-peptide docking, I would suggest using HADDOCK, ZDOCK softwares. They give good results.

regards

Tanuj

I believe that Snijesh V.P.'s comment contains good initial suggestions for your investigation, assuming that you are interested in macromolecular - small molecule binding affinity / conformation prediction. It may also be important to do proper binding site prediction, docking search space assessment, energy/geometry optimization of the macromolecular structure, careful consideration of specific Vina simulation parameters, and broader consideration of investigation parameters before initiating your simulation. Also, it is important that docking scores are contextualized properly when reported so that other researchers may be able to interpret them.

Thank you all (Snijesh, Tanuj , and Matthew) for your help and good sharing.

All the best,

Mostafa