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Benchmarking Sets for Molecular Docking
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Hi-Res PDFTo whom correspondence should be addressed. B.K.S: phone, 415-514-4126; fax, 415-514-4260; E-mail, shoichet@cgl.ucsf.edu. J.J.I: phone, 415-514-4127; fax, 415-514-4260; e-mail, jji@cgl.ucsf.edu.
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 http://blaster.docking.org/dud/.
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Accession Codes
- PDB: 1xq2
- PDB: 1l2i
- PDB: 3ert
- PDB: 1m2z
- PDB: 2aa2
- PDB: 1fm9
- PDB: 1sr7
- PDB: 1mvc
- PDB: 1ckp
- PDB: 1m17
- PDB: 1agw
- PDB: 1uy6
- PDB: 1kv2
- PDB: 2src
- PDB: 1kim
- PDB: 1vr2
- PDB: 1f0r
- PDB: 1ba8
- PDB: 1bju
- PDB: 1o86
- PDB: 1stw
- PDB: 1h1d
- PDB: 1xp0
- PDB: 3dfr
- PDB: 1c2t
- PDB: 1eve
- PDB: 1ah3
- PDB: 1xgj
- PDB: 1p4g
- PDB: 1cx2
- PDB: 1a8i
- PDB: 1hpx
- PDB: 1rt1
- PDB: 1hw8
- PDB: 1p44
- PDB: 1a4g
- PDB: 1efy
- PDB: 1b8o
- PDB: 1a7a
History
- Published In Issue November 16, 2006
- Received July 16, 2006
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