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DockoMatic \cite{Bullock_2013} provides a graphical user interface for setting up and analyzing AutoDock and AutoDock Vina docking jobs, including when run on a cluster. It also includes the ability to run inverse virtual screens (find proteins that bind a given ligand) and support for homology model construction.  DOVIS \cite{Jiang_2008} is an extension of AutoDock 4.0 that provides more efficient parallelization of large virtual screening jobs.  idock \cite{Li_2012} is a multi-threaded docking program that includes support for the AutoDock Vina scoring function and a random forest scoring function. I can output per-atom free energy information for hotspot detection.  MOLA \cite{Abreu_2010} is a pre-packaged distribution of AutoDock and AutoDock Vina for deployment on multi-platform computing clusters.