Assessing the similarity of ligand binding conformations with the Contact Mode Score

Comput Biol Chem. 2016 Oct:64:403-413. doi: 10.1016/j.compbiolchem.2016.08.007. Epub 2016 Sep 6.

Abstract

Structural and computational biologists often need to measure the similarity of ligand binding conformations. The commonly used root-mean-square deviation (RMSD) is not only ligand-size dependent, but also may fail to capture biologically meaningful binding features. To address these issues, we developed the Contact Mode Score (CMS), a new metric to assess the conformational similarity based on intermolecular protein-ligand contacts. The CMS is less dependent on the ligand size and has the ability to include flexible receptors. In order to effectively compare binding poses of non-identical ligands bound to different proteins, we further developed the eXtended Contact Mode Score (XCMS). We believe that CMS and XCMS provide a meaningful assessment of the similarity of ligand binding conformations. CMS and XCMS are freely available at http://brylinski.cct.lsu.edu/content/contact-mode-score and http://geaux-computational-bio.github.io/contact-mode-score/.

Keywords: CMS; Contact Mode Score; Ligand binding conformations; Molecular docking; RMSD; Root-mean-square deviation; XCMS; eXtended Contact Mode Score.

Publication types

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

MeSH terms

  • Binding Sites
  • Humans
  • Ligands
  • Models, Molecular*
  • Molecular Docking Simulation*
  • Particle Size
  • Protein Binding
  • Protein Structure, Tertiary

Substances

  • Ligands