MoMA-LigPath : a web server to simulate protein-ligand unbinding
Devaurs, Didier and Bouard, Léa and Vaisset, Marc and Zanon, Christophe and Al-Bluwi, Ibrahim and Iehl, Romain and Siméon, Thierry and Cortés, Juan (2013) MoMA-LigPath : a web server to simulate protein-ligand unbinding. Nucleic Acids Research, 41 (W1). W297-W302. ISSN 1362-4962 (https://doi.org/10.1093/nar/gkt380)
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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.
ORCID iDs
Devaurs, Didier ORCID: https://orcid.org/0000-0002-3415-9816, Bouard, Léa, Vaisset, Marc, Zanon, Christophe, Al-Bluwi, Ibrahim, Iehl, Romain, Siméon, Thierry and Cortés, Juan;-
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Item type: Article ID code: 90269 Dates: DateEvent1 July 2013Published11 May 2013Published Online18 April 2013AcceptedSubjects: Science > Natural history > Genetics
Science > Natural history > Biology
Science > Mathematics > Electronic computers. Computer scienceDepartment: Faculty of Science > Computer and Information Sciences Depositing user: Pure Administrator Date deposited: 16 Aug 2024 09:08 Last modified: 03 Oct 2024 09:39 URI: https://strathprints.strath.ac.uk/id/eprint/90269