Publications
2006
Moitessier N, Westhof E, Hanessian S
Docking of aminoglycosides to hydrated and flexible RNA Article de journal
Dans: J Med Chem, vol. 49, no. 3, p. 1023-1033, 2006, ISBN: 16451068, (0022-2623 (Print) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Molecular Nucleic Acid Conformation RNA/*chemistry Research Support, Non-U.S. Gov't Thermodynamics Water/*chemistry, Unité ARN, WESTHOF Aminoglycosides/*chemistry Anti-Bacterial Agents/*chemistry Crystallography, X-Ray *Models
@article{,
title = {Docking of aminoglycosides to hydrated and flexible RNA},
author = {N Moitessier and E Westhof and S Hanessian},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16451068},
isbn = {16451068},
year = {2006},
date = {2006-01-01},
journal = {J Med Chem},
volume = {49},
number = {3},
pages = {1023-1033},
abstract = {Although much effort has been devoted to the development of programs suited for the docking of ligands to proteins, much less progress has been achieved in the nucleic acid field. We have developed a unique approach for docking aminoglycosides to RNA considering the flexibility of these macromolecules using conformational ensembles and accounting for the role of the first hydration shell. This concept, successfully implemented in AutoDock, relies on the computation of the intermolecular interaction energy that accounts for the presence of dynamically bound water molecules to the RNA. As an application, a set of 11 aminoglycosides was docked with an average root-mean-square deviation (RMSD) of 1.41 A to be compared with an average RMSD of 3.25 A when the original AutoDock protocol was used.},
note = {0022-2623 (Print)
Journal Article},
keywords = {Molecular Nucleic Acid Conformation RNA/*chemistry Research Support, Non-U.S. Gov't Thermodynamics Water/*chemistry, Unité ARN, WESTHOF Aminoglycosides/*chemistry Anti-Bacterial Agents/*chemistry Crystallography, X-Ray *Models},
pubstate = {published},
tppubtype = {article}
}
Although much effort has been devoted to the development of programs suited for the docking of ligands to proteins, much less progress has been achieved in the nucleic acid field. We have developed a unique approach for docking aminoglycosides to RNA considering the flexibility of these macromolecules using conformational ensembles and accounting for the role of the first hydration shell. This concept, successfully implemented in AutoDock, relies on the computation of the intermolecular interaction energy that accounts for the presence of dynamically bound water molecules to the RNA. As an application, a set of 11 aminoglycosides was docked with an average root-mean-square deviation (RMSD) of 1.41 A to be compared with an average RMSD of 3.25 A when the original AutoDock protocol was used.