DOCK3.7 Documentation Wiki

This is the documentation wiki for UCSF DOCK 3.7, which is available at:

The main DOCK3.7 paper, please read & cite: Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013. Additional citations


mol2db2 and mol2db2 format

Ligand Preparation

Protein Target Preparation (Adding Static Waters to the Protein Structure) (Flexible Docking)

ZINC Subset DB2 file locations

Running DOCK

Analyzing DOCK Results

Auto-DUD-E Test Set (external site) Github mirror of Auto-DUD-E

Additional Tutorials

You may also be interested in the Teach-Discover-Treat 2014 tutorials, which used DOCK3.7 in a practical project for drug discovery and go through examples step-by-step. See the tutorials by Coleman & Karpiak:, &

All documentation on this wiki is under the following license:

This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported License. To view a copy of this license, visit

DOCK3.7 Documentation by Ryan G. Coleman is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License.

Based on a work at