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MoMA-LigPath: A web server to simulate protein-ligand unbinding

Didier Devaurs 1 Léa Bouard 1 Marc Vaisset 2 Christophe Zanon 2 Ibrahim Al Bluwi 1 Romain Iehl 1 Thierry Simeon 1 Juan Cortés 1
1 LAAS-RIS - Équipe Robotique et InteractionS
LAAS - Laboratoire d'analyse et d'architecture des systèmes
2 LAAS-IDEA - Service Informatique : Développement, Exploitation et Assistance
LAAS - Laboratoire d'analyse et d'architecture des systèmes
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 paper, 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 very short computing time. Ligand unbinding pathways generated by MoMA-LigPath are a first approximation that can provide very 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.
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Submitted on : Thursday, July 11, 2013 - 10:11:38 AM
Last modification on : Friday, July 3, 2020 - 4:28:24 PM
Long-term archiving on: : Saturday, October 12, 2013 - 4:55:08 AM

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Didier Devaurs, Léa Bouard, Marc Vaisset, Christophe Zanon, Ibrahim Al Bluwi, et al.. MoMA-LigPath: A web server to simulate protein-ligand unbinding. Nucleic Acids Research, Oxford University Press, 2013, vol. 41, pp. 297-302. ⟨10.1093/nar/gkt380⟩. ⟨hal-00843321⟩

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