{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T22:42:29Z","timestamp":1722811349444},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: We study a stochastic method for approximating the set of local minima in partial RNA folding landscapes associated with a bounded-distance neighbourhood of folding conformations. The conformations are limited to RNA secondary structures without pseudoknots. The method aims at exploring partial energy landscapes pL induced by folding simulations and their underlying neighbourhood relations. It combines an approximation of the number of local optima devised by Garnier and Kallel (2002) with a run-time estimation for identifying sets of local optima established by Reeves and Eremeev (2004).<\/jats:p>\n               <jats:p>Results: The method is tested on nine sequences of length between 50 nt and 400 nt, which allows us to compare the results with data generated by RNAsubopt and subsequent barrier tree calculations. On the nine sequences, the method captures on average 92% of local minima with settings designed for a target of 95%. The run-time of the heuristic can be estimated by O(n2D\u03bdln\u03bd), where n is the sequence length, \u03bd is the number of local minima in the partial landscape pL under consideration and D is the maximum number of steepest descent steps in attraction basins associated with pL.<\/jats:p>\n               <jats:p>Contact: \u00a0a.albrecht@qub.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr715","type":"journal-article","created":{"date-parts":[[2012,1,1]],"date-time":"2012-01-01T01:24:24Z","timestamp":1325381064000},"page":"523-530","source":"Crossref","is-referenced-by-count":5,"title":["Approximating the set of local minima in partial RNA folding landscapes"],"prefix":"10.1093","volume":"28","author":[{"given":"S.","family":"Sahoo","sequence":"first","affiliation":[{"name":"Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7BL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"A.A.","family":"Albrecht","sequence":"additional","affiliation":[{"name":"Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7BL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,12,30]]},"reference":[{"key":"2023012512181521000_B1","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1261\/rna.2125310","article-title":"ProbKnot: fast prediction of RNA secondary structure including pseudoknots","volume":"16","author":"Bellaousov","year":"2010","journal-title":"RNA"},{"key":"2023012512181521000_B2","doi-asserted-by":"crossref","first-page":"W154","DOI":"10.1093\/nar\/gkh352","article-title":"Riboswitch finder\u2013a tool for identification of riboswitch RNAs","volume":"32","author":"Bengert","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012512181521000_B3","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1146\/annurev.biophys.37.032807.125957","article-title":"RNA folding: Conformational statistics, folding kinetics, and ion electrostatics","volume":"37","author":"Chen","year":"2008","journal-title":"Annu. 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