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

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

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 pre...

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Bibliographic Details
Published in:Nucleic acids research Vol. 41; no. Web Server issue; pp. W297 - W302
Main Authors: Devaurs, Didier, Bouard, Léa, Vaisset, Marc, Zanon, Christophe, Al-Bluwi, Ibrahim, Iehl, Romain, Siméon, Thierry, Cortés, Juan
Format: Journal Article
Language:English
Published: England Oxford University Press 01-07-2013
Subjects:
Algorithms
Binding Sites
Biochemistry, Molecular Biology
Computer Science
Computer Simulation
Insulin - chemistry
Insulin - metabolism
Internet
Life Sciences
Ligands
Modeling and Simulation
Models, Molecular
Phenols - chemistry
Phenols - metabolism
Protein Conformation
Proteins - chemistry
Proteins - metabolism
Quantitative Methods
Robotics
Software
Structural Biology
Motion planning
Protein-ligand unbinding
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Summary: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.
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ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkt380