Resources from the Docking Community

Databases

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.

NCI Diversity Set is a set of several thousand compounds that represent the broader chemical space of the larger NCI compounds library. You can click here for the NCI-Diversity-AutoDock-0.2

BindingDB is a compilation of measured binding affinities of proteins with small drug-like compounds.

BindingMOAD was a curated subset of the PDB archive, containing all high-quality examples of ligand-protein complexes. The database is now obsolete. Read about its last update in this article: https://www.nature.com/articles/s41598-023-29996-w

Managing Protonation

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.