MoMA-LigPath: A web server to simulate protein-ligand unbinding - Archive ouverte HAL Access content directly
Journal Articles Nucleic Acids Research Year : 2013

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

(1) , (1) , (2) , (2) , (1) , (1) , (1) , (1)
1
2

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.
Fichier principal
Vignette du fichier
Devaurs_9222.pdf (230.56 Ko) Télécharger le fichier
Origin : Files produced by the author(s)
Loading...

Dates and versions

hal-00843321 , version 1 (11-07-2013)

Identifiers

Cite

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, 2013, vol. 41, pp. 297-302. ⟨10.1093/nar/gkt380⟩. ⟨hal-00843321⟩
234 View
154 Download

Altmetric

Share

Gmail Facebook Twitter LinkedIn More