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AutoDock Vina \cite{Trott_2009} is an entirely separate code base and approach from Autodock that was developed with a focus runtime performance and ease of system setup. It uses a fully empirical scoring function and an iterated local search global optimizer to produce docked poses. It includes support for multi-threading and flexible sidechains.  CADDP (computer-aided drug design platform) \cite{Lill_2010} is Clusterizer-DockAccessor are tools for accessing the quality of docking protocols. It interfaces with  a collection number  of plugins for PyMol for controlling and visualizing system setup (AMBER open-source  and Reduce) and docking (AutoDock Vina). free tools.  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.