Welcome to DUD•E, an enhanced and rebuilt version of DUD, a directory of useful decoys. DUD-E is designed to help benchmark molecular docking programs by providing challenging decoys. It contains:
- 22,886 active compounds and their affinities against 102 targets, an average of 224 ligands per target
- 50 decoys for each active having similar physico-chemical properties but dissimilar 2-D topology.
A newer version of DUDE is available! DUDE-Z is at dudez.docking.org
DUD-E is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). To cite DUD-E, please reference Mysinger MM, Carchia M, Irwin JJ, Shoichet BK J. Med. Chem., 2012, Jul 5. doi 10.1021/jm300687e .
We thank NIGMS for financial support (GM71896 to BKS and JJI). For correspondence about DUD-E, please write John Irwin jji at cgl dot ucsf dot edu.
DUD-E may be downloaded target-by-target, organized by subset such as GPCR and kinase, or all at once. You may also generate your own decoys.
DUD-E is a research tool which we have tried to make as useful and as correct as we know how. Anticipating that problems will undoubtedly be found, we have set up a DUDE wiki page and a DUDE Facebook page to allow the community to share problems or observations. We will endeavor to put right any problems promptly, as best we can.