Journal Article

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

Magdalena A. Jonikas, Randall J. Radmer and Russ B. Altman

in Bioinformatics

Volume 25, issue 24, pages 3259-3266
Published in print December 2009 | ISSN: 1367-4803
Published online October 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp576

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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 Article.  6296 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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