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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 MoMA-LigPath: A web server to simulate protein-ligand unbinding. (2013) Nucleic Acids Research, 41. 297-302. ISSN 0305-1048

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Official URL: http://dx.doi.org/10.1093/nar/gkt380

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.

Item Type:Article
Additional Information:Thanks to Oxford University Press editor.The definitive version is available at http://www.oxfordjournals.org The original PDF of the article can be found at Nucleic Acids Research website : http://dx.doi.org/10.1093/nar/gkt380
HAL Id:hal-00843321
Audience (journal):International peer-reviewed journal
Uncontrolled Keywords:
Institution:French research institutions > Centre National de la Recherche Scientifique - CNRS (FRANCE)
Université de Toulouse > Institut National Polytechnique de Toulouse - INPT (FRANCE)
Université de Toulouse > Institut National des Sciences Appliquées de Toulouse - INSA (FRANCE)
Université de Toulouse > Institut Supérieur de l'Aéronautique et de l'Espace - ISAE-SUPAERO (FRANCE)
Université de Toulouse > Université Toulouse III - Paul Sabatier - UPS (FRANCE)
Université de Toulouse > Université Toulouse - Jean Jaurès - UT2J (FRANCE)
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Deposited By: Didier Devaurs
Deposited On:08 Jul 2013 09:31

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