{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T13:28:01Z","timestamp":1774790881739,"version":"3.50.1"},"reference-count":59,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1937,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Accurate tertiary structures are very important for the functional study of non-coding RNA molecules. However, predicting RNA tertiary structures is extremely challenging, because of a large conformation space to be explored and lack of an accurate scoring function differentiating the native structure from decoys. The fragment-based conformation sampling method (e.g. FARNA) bears shortcomings that the limited size of a fragment library makes it infeasible to represent all possible conformations well. A recent dynamic Bayesian network method, BARNACLE, overcomes the issue of fragment assembly. In addition, neither of these methods makes use of sequence information in sampling conformations. Here, we present a new probabilistic graphical model, conditional random fields (CRFs), to model RNA sequence\u2013structure relationship, which enables us to accurately estimate the probability of an RNA conformation from sequence. Coupled with a novel tree-guided sampling scheme, our CRF model is then applied to RNA conformation sampling. Experimental results show that our CRF method can model RNA sequence\u2013structure relationship well and sequence information is important for conformation sampling. Our method, named as TreeFolder, generates a much higher percentage of native-like decoys than FARNA and BARNACLE, although we use the same simple energy function as BARNACLE.<\/jats:p>\n               <jats:p>Contact: \u00a0zywang@ttic.edu; j3xu@ttic.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr232","type":"journal-article","created":{"date-parts":[[2011,6,17]],"date-time":"2011-06-17T23:32:32Z","timestamp":1308353552000},"page":"i102-i110","source":"Crossref","is-referenced-by-count":12,"title":["A conditional random fields method for RNA sequence\u2013structure relationship modeling and conformation sampling"],"prefix":"10.1093","volume":"27","author":[{"given":"Zhiyong","family":"Wang","sequence":"first","affiliation":[{"name":"Toyota Technological Institute at Chicago, IL, USA"}]},{"given":"Jinbo","family":"Xu","sequence":"additional","affiliation":[{"name":"Toyota Technological Institute at Chicago, IL, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,6,14]]},"reference":[{"key":"2023012512015810300_B1","doi-asserted-by":"crossref","first-page":"2274","DOI":"10.1261\/rna.853208","article-title":"Analysis and classification of RNA tertiary structures","volume":"14","author":"Abraham","year":"2008","journal-title":"RNA"},{"key":"2023012512015810300_B2","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/S0166-218X(00)00186-4","article-title":"Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots","volume":"104","author":"Akutsu","year":"2000","journal-title":"Discrete Appl. 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