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Assessing the similarity of ligand binding conformations with the Contact Mode Score
Authors
Michal Brylinski
Yun Ding
+4 more
Ye Fang
Mark Jarrell
Juana Moreno
J. Ramanujam
Publication date
1 October 2016
Publisher
LSU Digital Commons
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Abstract
© 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/
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Louisiana State University
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Last time updated on 26/10/2023
Louisiana State University
See this paper in CORE
Go to the repository landing page
Download from data provider
oai:repository.lsu.edu:biosci_...
Last time updated on 26/10/2023