The molecular docking program AutoDock has been updated to version 4.
From the website:-
"The introduction of AutoDock 4 comprises three major improvements:

1. The docking results are more accurate and reliable.
2. It can optionally model flexibility in the target macromolecule.
3. It enables AutoDock's use in evaluating protein-protein interactions.

AutoDock 4.0  not only is it faster than earlier versions, it allows sidechains in the macromolecule to be flexible.  As before, rigid docking is blindingly fast, and high-quality flexible docking can be done in around a minute. Up to 40,000 rigid dockings can be done in a day on one cpu.
AutoDock 4.0 now has a free-energy scoring function that is based on a linear regression analysis, the AMBER force field, and an even larger set of diverse protein-ligand complexes with known inhibiton constants than we used in AutoDock 3.0. The best model was cross-validated with a separate set of HIV-1 protease complexes, and confirmed that the standard error is around 2.5 kcal/mol. This is enough to discriminate between leads with milli-, micro- and nano-molar inhibition constants."
Instructions for download are here