title: Predicting RNA 3D structure using a coarse-grain helix-centered model.
abstract: A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy and long running times and either neglect or presume knowledge of the long-range interactions which stabilize the tertiary structure. Our coarse-grained, helix-based, tertiary structure model operates with only a few degrees of freedom compared with all-atom models while preserving the ability to sample tertiary structures given a secondary structure. It strikes a balance between the precision of an all-atom tertiary structure model and the simplicity and effectiveness of a secondary structure representation. It provides a simplified tool for exploring global arrangements of helices and loops within RNA structures. We provide an example of a novel energy function relying only on the positions of stems and loops. We show that coupling our model to this energy function produces predictions as good as or better than the current state of the art tools. We propose that given the wide range of conformational space that needs to be explored, a coarse-grain approach can explore more conformations in less iterations than an all-atom model coupled to a fine-grain energy function. Finally, we emphasize the overarching theme of providing an ensemble of predicted structures, something which our tool excels at, rather than providing a handful of the lowest energy structures.
authors.affiliation: Institute for Theoretical Chemistry, A-1090 Vienna, Austria.
authors.forename: Peter
authors.initials: P
authors.lastname: Kerpedjiev
authors.affiliation: Institute for Theoretical Chemistry, A-1090 Vienna, Austria Bioinformatics Group, Department of Computer Science, Universität Leipzig, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Universität Leipzig, D-04107 Leipzig, Germany.
authors.forename: Christian
authors.identifier: http://orcid.org/0000-0001-9517-5839
authors.initials: C
authors.lastname: Höner Zu Siederdissen
authors.affiliation: Institute for Theoretical Chemistry, A-1090 Vienna, Austria Research Group Bioinformatics and Computational Biology, University of Vienna, A-1090 Vienna, Austria Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Science, University of Copenhagen, DK-1870 Frederiksberg, Denmark.
authors.forename: Ivo L
authors.identifier: http://orcid.org/0000-0001-7132-0800
authors.initials: IL
authors.lastname: Hofacker
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA
keywords: RNA tertiary structure; coarse-grain model; knowledge-based energy function; structure prediction