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      Benchmarking sets for molecular docking.

      Journal of Medicinal Chemistry

      Adenosine Deaminase, chemistry, Aldehyde Reductase, Binding Sites, Databases, Factual, Drug Design, Inhibins, Ligands, Models, Molecular, Pharmaceutical Preparations, Protein Binding, Protein Conformation, Proteins, Quantitative Structure-Activity Relationship, Receptors, Estrogen, antagonists & inhibitors, Thymidine Kinase, p38 Mitogen-Activated Protein Kinases

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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 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/.

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          Author and article information

          Journal
          17154509
          3383317
          10.1021/jm0608356

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