AutoDock is a suite of automated docking tools designed for molecular docking and it also allows sidechains in the macromolecule to be flexible. It is one of the most cited docking software in the research community and is maintained by the Scripps Research Institute.

AutoDock consists of mainly 2 programs:

• AutoDock: used for docking of the ligand to a set of grids that describes the target protein;
• AutoGrid: used for pre-calculation of these grids.

 

AutoDock Vina is the new generation of Autodock with significant improvements in speed and average accuracy of the binding mode prediction. Moreover, Autodock Vina internally calculates the grids for the atom types needed and therefore does not require choosing atom types and pre-calculating grid maps for them.

Applications: lead optimization, virtual screening (HTS), combinatorial library design, protein-protein docking, chemical mechanism studies etc.