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

Authors

Yun Ding, Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA 70803, USA. Electronic address: yding8@lsu.edu.
Ye Fang, School of Electrical Engineering and Computer Science, Louisiana State University, Baton Rouge, LA 70803, USA; Center for Computation & Technology, Louisiana State University, Baton Rouge, LA 70803, USA. Electronic address: yfang11@lsu.edu.
Juana Moreno, Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA 70803, USA; Center for Computation & Technology, Louisiana State University, Baton Rouge, LA 70803, USA. Electronic address: moreno@phys.lsu.edu.
J Ramanujam, School of Electrical Engineering and Computer Science, Louisiana State University, Baton Rouge, LA 70803, USA; Center for Computation & Technology, Louisiana State University, Baton Rouge, LA 70803, USA. Electronic address: ram@cct.lsu.edu.
Mark Jarrell, Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA 70803, USA; Center for Computation & Technology, Louisiana State University, Baton Rouge, LA 70803, USA. Electronic address: jarrellphysics@gmail.com.
Michal Brylinski, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; Center for Computation & Technology, Louisiana State University, Baton Rouge, LA 70803, USA. Electronic address: michal@brylinski.org.

Document Type

Article

Publication Date

10-1-2016

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/.

Publication Source (Journal or Book title)

Computational biology and chemistry

First Page

403

Last Page

413

Recommended Citation

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