| URL: | http://blaster.docking.org/dud/ |
| Full name: | directory of useful decoys |
| Description: | We have assembled a directory of useful decoys (DUD), with 2950 ligands for 40 different targets. Every ligand has 36 decoy molecules that are physically similar but topologically distinct, leading to a database of 98,266 compounds. |
| Year founded: | 2006 |
| Last update: | |
| Version: | |
| Accessibility: |
Accessible
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| Country/Region: | United States |
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| University/Institution: | University of California San Francisco |
| Address: | Department of Pharmaceutical Chemistry, University of California San Francisco, QB3 building, 1700 4th St., Box 2550, San Francisco, CA 94143-2550 U.S.A |
| City: | San Francisco |
| Province/State: | |
| Country/Region: | United States |
| Contact name (PI/Team): | John J. Irwin |
| Contact email (PI/Helpdesk): | jjicql@ucsf.edu |
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Benchmarking sets for molecular docking. [PMID: 17154509]
Ligand enrichment among top-ranking hits is a key metric of molecular docking. To avoid bias, decoys should resemble ligands physically, so that enrichment is not simply a separation of gross features, yet be chemically distinct from them, so that they are unlikely to be binders. We have assembled a directory of useful decoys (DUD), with 2950 ligands for 40 different targets. Every ligand has 36 decoy molecules that are physically similar but topologically distinct, leading to a database of 98,266 compounds. For most targets, enrichment was at least half a log better with uncorrected databases such as the MDDR than with DUD, evidence of bias in the former. These calculations also allowed 40x40 cross-docking, where the enrichments of each ligand set could be compared for all 40 targets, enabling a specificity metric for the docking screens. DUD is freely available online as a benchmarking set for docking at http://blaster.docking.org/dud/. |