DUD•E free to use and is provided by the Irwin and Shoichet Laboratories at 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.
You may also wish to cite the original version of DUD, Huang, Shoichet and Irwin, J. Med. Chem., 2006, 49(23), 6789-6801. doi 10.1021/jm0608356.
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This is not an official UCSF website. The opinions or statements expressed herein should not be taken as a position of or endorsement by the University of California, San Francisco.
Copyright 2009-2024 The Irwin Lab and the UC Regents
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:
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. To generate decoys for your own ligands, see Generate.
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.| Feature | DUD-E | Original DUD |
|---|---|---|
| Number of targets | 102 | 40 |
| Number of ligands per target | 100 to 600, 224 avg. | 11 to 475, 98 avg. |
| Decoys per ligand | 50 | 33 |
| Physical properties matched | Same as in DUD, plus net molecular charge | 5. Molecular weight, calculated LogP, H-bond donors and acceptors, number of rotatable bonds |
| Fingerprint and dissimilarity criteria | ECFP4, most 25% dissimilar | CACTVS default, 0.7 maximum (in retrospect, far too generous) |
| Clustering to downweight highly similar ligands | Yes | No |
| Literature references and affinities | Yes, via ChEMBL | No |
| Decoy maker available on-line for arbitrary active sets? | Yes, now via DUDE-Z | No |
You can write on our facebook page, http://facebook.com/dud You can write on our wiki, http://wiki.docking.org/index.php/DUDE You can join the mailing list decoys@docking.org and send to the group. You can write John Irwin jji at cgl dot ucsf dot edu.
| Release | Date | Comments |
|---|---|---|
| 1 | May 18th, 2012 | Initial Release, for review |
DUD-E would not be possible without the help of our colleages.
| Name | Release Date | Summary |
|---|---|---|
| Original DUD | October 22, 2006 | Huang, Shoichet and Irwin, J. Med. Chem., 2006, 49(23), 6789-6801. doi 10.1021/jm0608356 |
| GPCRs | December 21, 2015 | A collection of GPCR targets with decoys provided by Heptares |
The on-line DUD•E decoy generator has been retired from this website.
To generate property-matched decoys for your own active compounds, please use DUDE-Z, the newer version of DUD-E, and its decoy-generation tools at tldr.docking.org.
The pre-computed DUD•E decoys remain available for download target-by-target, organized by subset, or all at once.