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Primary Publication
Bioinformatics. 2009 Oct 7. Knowledge-Based Instantiation of Full Atomic Detail into Coarse Grain RNA 3D Structural Models. Jonikas MA, Radmer RJ, Altman RB. (2009)  View
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 (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 to 3.31 A 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 A 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 paper, are freely available at www.simtk.org/home/c2a.

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