autodock is quite good software for docking you also can use argus lab for docking both used genetic algorithm for docking. there are various other software and online tools like swissdock and pardock. pardock runs on Monte Carlo algorithm. i am using autodock.

Hi dear Kumar

Any docking software have advantage and disadvantage, in the fact any software use specially algorithm for Searching and Scoring so determine which of them is the best is not easy.

For began, Autodock  Vina is good. vina use Pseudorandom number and its popular software and its better than autodock 4.2 because its more accurate. vina generat binding affinity.

Other software like Gold(CCDC) , Glide(Schrodinger) are Good but they're not free .

bellow its good review about docking.

doi:10.1038/nrd1549

http://dx.doi.org/doi:10.1038/nrd1549

AutoDock is a good software for performing molecular docking. Its easy to use and you can follow using the steps in the manual below:

http://autodock.scripps.edu/faqs-help/manual/autodock-4-2-user-guide/AutoDock4.2.6_UserGuide.pdf

you can also try dock from Kuntz lab, a powerful tool... it is free for academic use.. you can use it with ucsf chimera tools...

http://sl.compbio.ucsf.edu/Online_Licensing/index.htm

Autodock

I would suggest you to try several docking programs, preferably using different scoring approaches, because it is highly case-dependent which program is better.

User friendly Auto dock is good and HEX 6.2 also you try. But HEX is slightly complected but you understood that is good one.

Dear all,

Thank you so much.

Can we use autodock for docking a carbon nanostructure with a drug or a protein molecule???

When I downloaded the vina MSI file I could not run it. Kindly suggest me the steps for download and also attach some video if you have related to docking.

@Janani Kumar,

If you are thinking in docking that type of systems (carbon nanostructure+something), I recommend you to use other techniques like Quantum Mechanics/Molecular Mechanics (QM/MM), Fragment Molecular Orbital (FMO) or structural optimizations using semi-empirical methods (i.e. MOPAC+MOZIME).

These methods are "generic" whereas docking program complains about using a ligand that it is not a "common" drug-like ligand.

Best,

Camps

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

By using MOE program, i obtained more than 85% result, byusing this way exactly

https://www.youtube.com/watch?v=gD2ECxh-3BQ