title: Coarse-grained modeling of RNA 3D structure.
abstract: Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result.
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland. Electronic address: wdawson@genesilico.pl.
authors.forename: Wayne K
authors.initials: WK
authors.lastname: Dawson
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland; Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 4, 10-719 Olsztyn, Poland.
authors.forename: Maciej
authors.initials: M
authors.lastname: Maciejczyk
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland.
authors.forename: Elzbieta J
authors.initials: EJ
authors.lastname: Jankowska
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland; Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland. Electronic address: iamb@genesilico.pl.
authors.forename: Janusz M
authors.initials: JM
authors.lastname: Bujnicki
mesh_terms: D001483:Base Sequence; D030561:Databases, Nucleic Acid; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D012313:RNA
keywords: Bioinformatics; Modeling; Molecular dynamics; Monte Carlo dynamics; RNA; Simulation; Structure