title: Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings.
abstract: HiRE-RNA is a coarse-grained model for RNA structure prediction and the dynamical study of RNA folding. Using a reduced set of particles and detailed interactions accounting for base-pairing and stacking, we show that noncanonical and multiple base interactions are necessary to capture the full physical behavior of complex RNAs. In this paper, we give a full account of the model and present results on the folding, stability, and free energy surfaces of 16 systems with 12 to 76 nucleotides of increasingly complex architectures, ranging from monomers to dimers, using a total of 850 μs of simulation time.
authors.affiliation: Laboratoire de Biochimie Théorique UPR 9080 CNRS, Université Paris Diderot , Sorbonne, Paris Cité, IBPC 13 rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Tristan
authors.initials: T
authors.lastname: Cragnolini
authors.affiliation: Laboratoire de Biochimie Théorique UPR 9080 CNRS, Université Paris Diderot , Sorbonne, Paris Cité, IBPC 13 rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Yoann
authors.initials: Y
authors.lastname: Laurin
authors.affiliation: Laboratoire de Biochimie Théorique UPR 9080 CNRS, Université Paris Diderot , Sorbonne, Paris Cité, IBPC 13 rue Pierre et Marie Curie, 75005 Paris, France.|Institut Universitaire de France , Boulevard Saint-Michel, 75005 Paris, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Derreumaux
authors.affiliation: Laboratoire de Biochimie Théorique UPR 9080 CNRS, Université Paris Diderot , Sorbonne, Paris Cité, IBPC 13 rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Samuela
authors.initials: S
authors.lastname: Pasquali
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D056004:Molecular Dynamics Simulation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D059370:RNA Folding; D013696:Temperature; D013816:Thermodynamics
chemical_list: D012313:RNA