DUD
A Directory of Useful Decoys
Welcome to DUD, a directory of useful decoys for benchmarking virtual screening. DUD is designed to help test docking algorithms by providing challenging decoys. It contains:
  • A total of 2,950 active compounds against a total of 40 targets
  • For each active, 36 "decoys" with similar physical properties (e.g. molecular weight, calculated LogP) but dissimilar topology.
DUD is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). To cite DUD, please reference Huang, Shoichet and Irwin, J. Med. Chem., 2006, 49(23), 6789-6801. doi 10.1021/jm0608356. There is a DUD wiki page where you can discuss DUD and an errata page where problems are reported and explained. We aim to fix all problems in the next release. We thank NIGMS for financial support (GM71896). For correspondence about DUD, please write John Irwin jji at cgl dot ucsf dot edu.

Go to Download Page

DUD is drawn from ZINC, a database of commerically available compounds for virtual screening, so compounds in DUD are purchasable, although some may become depleted over time. You may download DUD either in packages (some of which are large!) or you may browse the files and download them individually. Anticipating that problems will be found, and corrected, in DUD, we number our releases as follows:


ReleaseDateComments
1 Oct 1, 2006 Original release
2 Oct 22, 2006 Proofreading corrections accompanying
the final manuscript.

DUD-related datasets

Charge Matched DUD Sep 27, 2010 Version of DUD adding net charge to the property matching. If you use it, please cite:

Mysinger, M. M.; Shoichet, B. K. "Rapid Context-Dependent Ligand Desolvation in Molecular Docking" J Chem Inf Model 50:1561-73 (2010). DOI: 10.1021/ci100214a

DUD Clusters Aug 27, 2007 Clustering from Andrew Good presented at the August 2007 ACS meeting
WOMBAT Data for Enrichment Studies Aug 27, 2007. WOMBAT Datasets for Enrichment Studies (presented by Andrew Good at Boston ACS Aug 2007). WOMBAT courtesy of Sunset Molecular publishers of WOMBAT.

If you use this data, please cite the following: Good AC and Oprea TI, "Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?", J. Comput. Aided Mol. Des. 2008, 22: 169-78.

JMC2008-water Jun 20, 2008 Huang and Shoichet, J Med Chem, 2008, docking with variable water structure
DUD LIB VS 1.0 Jul 8, 2009 DUD subsets for ligand-based virtual screening. Jahn, Hinselmann, Fechner and Zell, "Optimal assignment methods for ligand-based virtual screening", Journal of Cheminformatics, 2009, 1, 14. Readme file
Partial Charges for DUD Molecules recalculated by Inhibox July 13, 2010 Local mirror of files
Inhibox website