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

Magdalena A. Jonikas,R. J. Radmer,Russ B. Altman

Published 2009 in Bioinform.

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

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