Assessing the similarity of ligand binding conformations with the Contact Mode Score.
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/.
Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA 70803, USA. Electronic address: yding8@lsu.edu.
Yun
Y
Ding
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.
Ye
Y
Fang
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.
Juana
J
Moreno
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.
J
J
Ramanujam
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.
Mark
M
Jarrell
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.
Michal
M
Brylinski
D001665:Binding Sites; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D010316:Particle Size; D011485:Protein Binding; D017434:Protein Structure, Tertiary
D008024:Ligands
CMS; Contact Mode Score; Ligand binding conformations; Molecular docking; RMSD; Root-mean-square deviation; XCMS; eXtended Contact Mode Score