Benchmarking sets for molecular docking

J Med Chem. 2006 Nov 16;49(23):6789-801. doi: 10.1021/jm0608356.


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

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

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


  • Ligands
  • Pharmaceutical Preparations
  • Proteins
  • Receptors, Estrogen
  • inhibin-alpha subunit
  • Inhibins
  • Aldehyde Reductase
  • Thymidine Kinase
  • p38 Mitogen-Activated Protein Kinases
  • Adenosine Deaminase