AutoDock

AutoDock is a suite of automated ligand docking tools. In the recent years AutoDock is the most cited docking program. AutoDock actually consists of two main programs: AutoDock performs the docking of the ligand to a grids describing the target set of protein; AutoGrid pre-calculates these grids.

AutoDock has graphical user interface called AutoDockTools (ADT). You can use ADT to set up, run and analyze AutoDock docking and isocontour AutoGrid affinity maps, as well as compute molecular surfaces, display secondary structure ribbons, compute hydrogen-bonds, etc.

Another very useful interface to AutoDock is open in new windowBDT. BDT is an graphic front-end application for automation massive docking tasks such as virtual screening and blind docking.
AutoDock Web site Home page.