title: Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints.
abstract: A novel protocol for all-atom RNA tertiary structure prediction is presented that uses restrained molecular mechanics and simulated annealing. The restraints are from secondary structure, covariation analysis, coaxial stacking predictions for helices in junctions, and, when available, cross-linking data. Results are demonstrated on the Alu domain of the mammalian signal recognition particle RNA, the Saccharomyces cerevisiae phenylalanine tRNA, the hammerhead ribozyme, the hepatitis C virus internal ribosomal entry site, and the P4-P6 domain of the Tetrahymena thermophila group I intron. The predicted structure is selected from a pool of decoy structures with a score that maximizes radius of gyration and base-base contacts, which was empirically found to select higher quality decoys. This simple ab initio approach is sufficient to make good predictions of the structure of RNAs compared to current crystal structures using both root mean square deviation and the accuracy of base-base contacts.
authors.affiliation: Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642.
authors.forename: Matthew G
authors.initials: MG
authors.lastname: Seetin
authors.forename: David H
authors.initials: DH
authors.lastname: Mathews
mesh_terms: D007438:Introns; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D016337:RNA, Catalytic / Q000737:chemistry; D012360:RNA, Transfer, Phe / Q000737:chemistry; D018271:Signal Recognition Particle / Q000737:chemistry
chemical_list: D016337:RNA, Catalytic; D012360:RNA, Transfer, Phe; D018271:Signal Recognition Particle; C427204:hammerhead ribozyme; D012313:RNA