Resources from the Docking Community
Protein Data Bank is the primary archive of biomolecular structure, including many structures of biomolecules with bound ligands.
Zinc is a free database of commercially-available compounds for virtual screening and a great source of small molecule structures for AutoDock.
BindingDB is a compilation of measured binding affinities of proteins with small drug-like compounds.
BindingMOAD is a curated subset of the PDB archive, containing all high-quality examples of ligand-protein complexes.
Reduce adds hydrogen positions to PDB files using standardized geometry with optimized orientations.
Setup and Visualization
UCSF Chimera includes setup tools for AutoDock Vina, and many options for visualization.
Daniel Seeliger has an Autodock/Vina plugin for PyMOL.