title: GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.
abstract: Cellular processes involve large numbers of RNA molecules. The functions of these RNA molecules and their binding to molecular machines are highly dependent on their 3D structures. One of the key challenges in RNA structure prediction and modeling is predicting the spatial arrangement of the various structural elements of RNA. As RNA folding is generally hierarchical, methods involving coarse-grained models hold great promise for this purpose. We present here a novel coarse-grained method for sampling, based on game theory and knowledge-based potentials. This strategy, GARN (Game Algorithm for RNa sampling), is often much faster than previously described techniques and generates large sets of solutions closely resembling the native structure. GARN is thus a suitable starting point for the molecular modeling of large RNAs, particularly those with experimental constraints. GARN is available from: http://garn.lri.fr/.
authors: PRiSM, CNRS UMR 8144, Université de Versailles-St-Quentin-en-Yvelines, 78000 Versailles, France; LRI, CNRS UMR 8623, Université Paris-Sud, 91405 Orsay, France.
authors: Mélanie
authors: M
authors: Boudard
authors: AMIB, Inria Saclay-Ile de France, 91120 Palaiseau, France; LIX, CNRS UMR 7161, Ecole Polytechnique, 91120 Palaiseau, France.
authors: Julie
authors: J
authors: Bernauer
authors: PRiSM, CNRS UMR 8144, Université de Versailles-St-Quentin-en-Yvelines, 78000 Versailles, France.
authors: Dominique
authors: D
authors: Barth
authors: LRI, CNRS UMR 8623, Université Paris-Sud, 91405 Orsay, France.
authors: Johanne
authors: J
authors: Cohen
authors: LRI, CNRS UMR 8623, Université Paris-Sud, 91405 Orsay, France; AMIB, Inria Saclay-Ile de France, 91120 Palaiseau, France; I2BC, CNRS, Université Paris-Sud, 91405 Orsay, France.
authors: Alain
authors: A
authors: Denise
mesh_terms: D000465:Algorithms; D005716:Game Theory; D051188:Knowledge Bases; D008958:Models, Molecular; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding
chemical_list: D012313:RNA