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


BACKGROUND
Code for the C2A method, as well as the examples discussed in this article, are freely available at www.simtk.org/home/c2a.


BACKGROUND
russ.altman@stanford.edu
Jonikas
Magdalena A
MA
Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Radmer
Randall J
RJ
Altman
Russ B
RB
D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D051188:Knowledge Bases; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
D012313:RNA