I am going to try autodock. Anyone here on friendfeed has a better suggestion ? - Pedro Beltrao

Autodock would be my recommendation as well unless there is something new out there that I haven't tracked. - Deepak Singh

Autodock seems to be widely-used and well-regarded. Could also try zdock - more lightweight and good for command-line scripting, parsing. - Neil Saunders

zdock is more protein-protein centric. Did they add small molecule stuff? - Deepak Singh from IM

Ah, that's true. Haven't used it in a while. Autodock would be better for ligands. - Neil Saunders

wondering how difficult it would be to integrate #autodock into #bioclipse or with the #cdk ... - Egon Willighagen

can Autodock actually be scripted from the command line? Or am I restricted to using their GUI to create input files? - Egon Willighagen

I believe they had developed a python based framework - Deepak Singh from IM

they have command line tools but I am still wrapping my head around the basics - Pedro Beltrao

FRED (not Open Source) is very easy to use, but maybe not as accurate as others. If accuracy is the goal it seems that Glide does a good job. - Rajarshi Guha

Glide is definitely state of the art. The one thing about docking though is no one tool is good enough. Pretty much every company I know that does a lot of virtual screening uses two tools - Deepak Singh from IM

Thanks for the suggestions. Does anyone know if Glide free for academics ? - Pedro Beltrao