Exploiting ordered waters in molecular docking

J Med Chem. 2008 Aug 28;51(16):4862-5. doi: 10.1021/jm8006239. Epub 2008 Aug 5.


A current weakness in docking is the treatment of water-mediated protein-ligand interactions. We explore switching ordered water molecules "on" and "off" during docking screens of a large library. The method assumes additivity and scales linearly with the number of waters sampled despite the exponential growth in configurations. It is tested for ligand enrichment against 24 targets, exploring up to 256 water configurations. Water inclusion increased enrichment substantially for 12 targets, while most others were largely unaffected.

Publication types

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

MeSH terms

  • Binding Sites
  • Computer Simulation
  • Ligands
  • Models, Molecular
  • Protein Binding*
  • Water / chemistry*


  • Ligands
  • Water