title: ProbKnot: fast prediction of RNA secondary structure including pseudoknots.
abstract: It is a significant challenge to predict RNA secondary structures including pseudoknots. Here, a new algorithm capable of predicting pseudoknots of any topology, ProbKnot, is reported. ProbKnot assembles maximum expected accuracy structures from computed base-pairing probabilities in O(N(2)) time, where N is the length of the sequence. The performance of ProbKnot was measured by comparing predicted structures with known structures for a large database of RNA sequences with fewer than 700 nucleotides. The percentage of known pairs correctly predicted was 69.3%. Additionally, the percentage of predicted pairs in the known structure was 61.3%. This performance is the highest of four tested algorithms that are capable of pseudoknot prediction. The program is available for download at: http://rna.urmc.rochester.edu/RNAstructure.html.
authors.affiliation: Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA.
authors.forename: Stanislav
authors.initials: S
authors.lastname: Bellaousov
authors.forename: David H
authors.initials: DH
authors.lastname: Mathews
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology; D003198:Computer Simulation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics; D012984:Software; D016963:Thermus thermophilus / Q000235:genetics
chemical_list: D012329:RNA, Bacterial; D012313:RNA