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Benchmarking Sets for Molecular Docking
| Venue: | J. Med. Chem |
| Citations: | 76 - 4 self |
BibTeX
@ARTICLE{Huang_benchmarkingsets,
author = {Niu Huang and Brian K. Shoichet and John J. Irwin},
title = {Benchmarking Sets for Molecular Docking},
journal = {J. Med. Chem},
year = {},
pages = {6789--6801}
}
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Abstract
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 40 40 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
