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Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models

Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models Motivation: The recent development of methods for modeling RNA 3D structures using coarse-grain approaches creates a need to bridge low- and high-resolution modeling methods. Although they contain topological information, coarse-grain models lack atomic detail, which limits their utility for some applications.Results: We have developed a method for adding full atomic detail to coarse-grain models of RNA 3D structures. Our method [Coarse to Atomic (C2A)] uses geometries observed in known RNA crystal structures. Our method rebuilds full atomic detail from ideal coarse-grain backbones taken from crystal structures to within 1.87–3.31 Å RMSD of the full atomic crystal structure. When starting from coarse-grain models generated by the modeling tool NAST, our method builds full atomic structures that are within 1.00 Å RMSD of the starting structure. The resulting full atomic structures can be used as starting points for higher resolution modeling, thus bridging high- and low-resolution approaches to modeling RNA 3D structure.Availability: Code for the C2A method, as well as the examples discussed in this article, are freely available at www.simtk.org/home/c2a.Contact: russ.altman@stanford.edu http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Bioinformatics Oxford University Press

Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models

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References (44)

Publisher
Oxford University Press
Copyright
© The Author(s) 2009. Published by Oxford University Press.
ISSN
1367-4803
eISSN
1460-2059
DOI
10.1093/bioinformatics/btp576
pmid
19812110
Publisher site
See Article on Publisher Site

Abstract

Motivation: The recent development of methods for modeling RNA 3D structures using coarse-grain approaches creates a need to bridge low- and high-resolution modeling methods. Although they contain topological information, coarse-grain models lack atomic detail, which limits their utility for some applications.Results: We have developed a method for adding full atomic detail to coarse-grain models of RNA 3D structures. Our method [Coarse to Atomic (C2A)] uses geometries observed in known RNA crystal structures. Our method rebuilds full atomic detail from ideal coarse-grain backbones taken from crystal structures to within 1.87–3.31 Å RMSD of the full atomic crystal structure. When starting from coarse-grain models generated by the modeling tool NAST, our method builds full atomic structures that are within 1.00 Å RMSD of the starting structure. The resulting full atomic structures can be used as starting points for higher resolution modeling, thus bridging high- and low-resolution approaches to modeling RNA 3D structure.Availability: Code for the C2A method, as well as the examples discussed in this article, are freely available at www.simtk.org/home/c2a.Contact: russ.altman@stanford.edu

Journal

Bioinformatics – Oxford University Press

Published: Oct 7, 2009

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