Similarity based docking

J Chem Inf Model. 2008 Jan;48(1):186-96. doi: 10.1021/ci700124r. Epub 2007 Nov 29.


We have recently introduced GMA, a highly efficient method for flexible molecular alignment. Here we show how this approach can be used to improve docking accuracy and efficiency, in cases where a complex structure of a ligand with the target protein is known. In cases where a known ligand exists, yet the complex structure is unknown it is possible to make use of the advantages offered by this approach, by combining it with standard ligand docking.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Crystallography, X-Ray
  • Ligands
  • Models, Chemical*
  • Models, Molecular
  • Proteins / chemistry*
  • Proteins / metabolism*
  • Reproducibility of Results
  • Time Factors


  • Ligands
  • Proteins