MoMA-LigPath: a web server to simulate protein-ligand unbinding.

Didier Devaurs, Léa Bouard, Marc Vaisset, Christophe Zanon, Ibrahim Al-Bluwi, Romain Iehl, Thierry Siméon, Juan Cortés

Research output: Contribution to journalArticle

23 Scopus citations

Abstract

Protein-ligand interactions taking place far away from the active site, during ligand binding or release, may determine molecular specificity and activity. However, obtaining information about these interactions with experimental or computational methods remains difficult. The computational tool presented in this article, MoMA-LigPath, is based on a mechanistic representation of the molecular system, considering partial flexibility, and on the application of a robotics-inspired algorithm to explore the conformational space. Such a purely geometric approach, together with the efficiency of the exploration algorithm, enables the simulation of ligand unbinding within short computing time. Ligand unbinding pathways generated by MoMA-LigPath are a first approximation that can provide useful information about protein-ligand interactions. When needed, this approximation can be subsequently refined and analyzed using state-of-the-art energy models and molecular modeling methods. MoMA-LigPath is available at http://moma.laas.fr. The web server is free and open to all users, with no login requirement.

Original languageEnglish (US)
Pages (from-to)W297-302
JournalUnknown Journal
Volume41
Issue numberWeb Server issue
DOIs
StatePublished - Jul 2013

All Science Journal Classification (ASJC) codes

  • Genetics

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    Devaurs, D., Bouard, L., Vaisset, M., Zanon, C., Al-Bluwi, I., Iehl, R., Siméon, T., & Cortés, J. (2013). MoMA-LigPath: a web server to simulate protein-ligand unbinding. Unknown Journal, 41(Web Server issue), W297-302. https://doi.org/10.1093/nar/gkt380