title: MoMA-LigPath: a web server to simulate protein-ligand unbinding.
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.
authors.affiliation: CNRS, LAAS, 7 av du colonel Roche, F-31400 Toulouse, France.
authors.forename: Didier
authors.initials: D
authors.lastname: Devaurs
authors.forename: Léa
authors.initials: L
authors.lastname: Bouard
authors.forename: Marc
authors.initials: M
authors.lastname: Vaisset
authors.forename: Christophe
authors.initials: C
authors.lastname: Zanon
authors.forename: Ibrahim
authors.initials: I
authors.lastname: Al-Bluwi
authors.forename: Romain
authors.initials: R
authors.lastname: Iehl
authors.forename: Thierry
authors.initials: T
authors.lastname: Siméon
authors.forename: Juan
authors.initials: J
authors.lastname: Cortés
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D007328:Insulin / Q000737:chemistry / Q000378:metabolism; D020407:Internet; D008024:Ligands; D008958:Models, Molecular; D010636:Phenols / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software
chemical_list: D007328:Insulin; D008024:Ligands; D010636:Phenols; D011506:Proteins