Automated identification of crystallographic ligands using sparse-density representations

Acta Crystallogr D Biol Crystallogr. 2014 Jul;70(Pt 7):1844-53. doi: 10.1107/S1399004714008578. Epub 2014 Jun 29.


A novel procedure for the automatic identification of ligands in macromolecular crystallographic electron-density maps is introduced. It is based on the sparse parameterization of density clusters and the matching of the pseudo-atomic grids thus created to conformationally variant ligands using mathematical descriptors of molecular shape, size and topology. In large-scale tests on experimental data derived from the Protein Data Bank, the procedure could quickly identify the deposited ligand within the top-ranked compounds from a database of candidates. This indicates the suitability of the method for the identification of binding entities in fragment-based drug screening and in model completion in macromolecular structure determination.

Keywords: drug design; ligands; macromolecular X-ray crystallography; shape descriptors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Automation*
  • Crystallography, X-Ray / methods*
  • Databases, Protein
  • Ligands


  • Ligands