© 2016 Elsevier Ltd 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/.
Publication Source (Journal or Book title)
Computational Biology and Chemistry
Ding, Y., Fang, Y., Moreno, J., Ramanujam, J., Jarrell, M., & Brylinski, M. (2016). Assessing the similarity of ligand binding conformations with the Contact Mode Score. Computational Biology and Chemistry, 64, 403-413. https://doi.org/10.1016/j.compbiolchem.2016.08.007