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Benchmarking sets for molecular docking
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AI
DOI：10.1021/jm0608356.png)
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摘要
En 中文
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 x 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/.
Keyword:
STRUCTURE-BASED DISCOVERY
STRUCTURE-BASED DESIGN
SCORING FUNCTIONS
AUTOMATED DOCKING
LIGAND DOCKING
BINDING-SITE
INHIBITORS
DATABASE
POTENT
KINASE
期刊
IF:
6.8
论文数:
2.7W
被引数:
9.4W
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