title: Modeling and predicting RNA three-dimensional structures.
abstract: Modeling the three-dimensional structure of RNAs is a milestone toward better understanding and prediction of nucleic acids molecular functions. Physics-based approaches and molecular dynamics simulations are not tractable on large molecules with all-atom models. To address this issue, coarse-grained models of RNA three-dimensional structures have been developed. In this chapter, we describe a graphical modeling based on the Leontis-Westhof extended base-pair classification. This representation of RNA structures enables us to identify highly conserved structural motifs with complex nucleotide interactions in structure databases. Further, we show how to take advantage of this knowledge to quickly and simply predict three-dimensional structures of large RNA molecules.
authors.affiliation: School of Computer Science, McGill University, 3480 University Street, Room 318, Montreal, QC, Canada, H3A 0E9, jeromew@cs.mcgill.ca.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Waldispühl
authors.forename: Vladimir
authors.initials: V
authors.lastname: Reinharz
mesh_terms: D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012984:Software
chemical_list: D012313:RNA