| Docking of aminoglycosides to hydrated and flexible RNA. | |
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MedLine Citation:
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PMID: 16451068 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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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. |
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Authors:
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Nicolas Moitessier; Eric Westhof; Stephen Hanessian |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't |
Journal Detail:
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Title: Journal of medicinal chemistry Volume: 49 ISSN: 0022-2623 ISO Abbreviation: J. Med. Chem. Publication Date: 2006 Feb |
Date Detail:
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Created Date: 2006-02-02 Completed Date: 2006-03-29 Revised Date: 2006-11-15 |
Medline Journal Info:
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Nlm Unique ID: 9716531 Medline TA: J Med Chem Country: United States |
Other Details:
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Languages: eng Pagination: 1023-33 Citation Subset: IM |
Affiliation:
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Department of Chemistry, McGill University, 801 Sherbrooke Street W, Montréal, Québec H3A 2K6, Canada. nicolas.moitessier@mcgill.ca |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Aminoglycosides
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chemistry* Anti-Bacterial Agents / chemistry* Crystallography, X-Ray Models, Molecular* Nucleic Acid Conformation RNA / chemistry* Thermodynamics Water / chemistry* |
| Chemical | |
Reg. No./Substance:
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0/Aminoglycosides; 0/Anti-Bacterial Agents; 63231-63-0/RNA; 7732-18-5/Water |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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