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

TitleAssessing the similarity of ligand binding conformations with the Contact Mode Score
Publication TypeJournal Article
Year of Publication2016
AuthorsDing Y, Fang Y, Moreno J, Ramanujam J, Jarrell M, Brylinski M
JournalComput Biol Chem
Volume64
Pagination403-413
Date Published2016 Sep 6
ISSN1476-928X
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/.

DOI10.1016/j.compbiolchem.2016.08.007
Alternate JournalComputational Biology and Chemistry
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