MED-3DMC: a new tool to generate 3D conformation ensembles of small molecules with a Monte Carlo sampling of the conformational space

Eur J Med Chem. 2009 Apr;44(4):1405-9. doi: 10.1016/j.ejmech.2008.09.052. Epub 2008 Oct 21.


Obtaining an efficient sampling of the low to medium energy regions of a ligand conformational space is of primary importance for getting insight into relevant binding modes of drug candidates, or for the screening of rigid molecular entities on the basis of a predefined pharmacophore or for rigid body docking. Here, we report the development of a new computer tool that samples the conformational space by using the Metropolis Monte Carlo algorithm combined with the MMFF94 van der Waals energy term. The performances of the program have been assessed on 86 drug-like molecules that resulted from an ADME/tox profiling applied on cocrystalized small molecules and were compared with the program Omega on the same dataset. Our program has also been assessed on the 85 molecules of the Astex diverse set. Both test sets show convincing performance of our program at sampling the conformational space.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Crystallography, X-Ray
  • Ligands
  • Models, Molecular
  • Molecular Conformation*
  • Monte Carlo Method*
  • Reproducibility of Results
  • Small Molecule Libraries / chemistry*


  • Ligands
  • Small Molecule Libraries