title: Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models.
abstract: 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
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
authors.forename: Magdalena A
authors.initials: MA
authors.lastname: Jonikas
authors.forename: Randall J
authors.initials: RJ
authors.lastname: Radmer
authors.forename: Russ B
authors.initials: RB
authors.lastname: Altman
mesh_terms: 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*
chemical_list: D012313:RNA