yes, you can. Now many software such as AutoDock, DOCK, FRED, Surflex, FlexX, Glide, GOLD, ICMc, MVD ,MOE et. al can used to molecular docking. You can choose one.

@Qiang We: What are the adavantages when you use AUTODOCK?

Sorry, when I docking ligand and receptor used AUTODOCK , I found the ligand didn't locate in pocket, so I don't know how can I do.

Hi Arun,

For protein-ligand docking the Autodock4.2 is best suited because of the accuracy and also with the features it has been provided in it for docking. The positive point of Autodock4.2 is its a freeware where as other softwares which have comparable accuracy such MVD, Glide etc are paid ones. So this gives Autodock4.2 a better position than anyother software in the range.

Cheers!!

@Anupam: Does Autodock4.2 work on windows? Or is there a way to make it work?

Arun,

Yes! you can install it on windows. I will suggest use linux for it because that way your simulations will run faster in comparison to windows.

Cheers!

hi pls try HEX tool for docking studies

Thank you R. Shalini