{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T05:36:56Z","timestamp":1767850616099,"version":"3.49.0"},"reference-count":31,"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>Motivation: RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment.<\/jats:p>\n               <jats:p>Results: We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of programs for parameter optimization and structure prediction.<\/jats:p>\n               <jats:p>Availability: All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at www.tbi.univie.ac.at\/software\/rnawolf\/.<\/jats:p>\n               <jats:p>Contact: \u00a0choener@tbi.univie.ac.at<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr220","type":"journal-article","created":{"date-parts":[[2011,6,17]],"date-time":"2011-06-17T23:32:32Z","timestamp":1308353552000},"page":"i129-i136","source":"Crossref","is-referenced-by-count":62,"title":["A folding algorithm for extended RNA secondary structures"],"prefix":"10.1093","volume":"27","author":[{"given":"Christian H\u00f6ner","family":"zu Siederdissen","sequence":"first","affiliation":[{"name":"1 Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria, 2Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, 3Max Planck Institute for Mathematics in the Sciences, 4RNomics Group, Fraunhofer IZI, D-04103 Leipzig, Germany, 5Center for Non\u2212Coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, DK-1870 Frederiksberg, Denmark and 6The Santa Fe Institute, Santa Fe, 87501 NM, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephan H.","family":"Bernhart","sequence":"additional","affiliation":[{"name":"1 Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria, 2Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, 3Max Planck Institute for Mathematics in the Sciences, 4RNomics Group, Fraunhofer IZI, D-04103 Leipzig, Germany, 5Center for Non\u2212Coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, DK-1870 Frederiksberg, Denmark and 6The Santa Fe Institute, Santa Fe, 87501 NM, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter F.","family":"Stadler","sequence":"additional","affiliation":[{"name":"1 Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria, 2Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, 3Max Planck Institute for Mathematics in the Sciences, 4RNomics Group, Fraunhofer IZI, D-04103 Leipzig, Germany, 5Center for Non\u2212Coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, DK-1870 Frederiksberg, Denmark and 6The Santa Fe Institute, Santa Fe, 87501 NM, USA"},{"name":"1 Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria, 2Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, 3Max Planck Institute for Mathematics in the Sciences, 4RNomics Group, Fraunhofer IZI, D-04103 Leipzig, Germany, 5Center for Non\u2212Coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, DK-1870 Frederiksberg, Denmark and 6The Santa Fe Institute, Santa Fe, 87501 NM, USA"},{"name":"1 Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria, 2Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, 3Max Planck Institute for Mathematics in the Sciences, 4RNomics Group, Fraunhofer IZI, D-04103 Leipzig, Germany, 5Center for Non\u2212Coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, DK-1870 Frederiksberg, Denmark and 6The Santa Fe Institute, Santa Fe, 87501 NM, USA"},{"name":"1 Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria, 2Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, 3Max Planck Institute for Mathematics in the Sciences, 4RNomics Group, Fraunhofer IZI, D-04103 Leipzig, Germany, 5Center for Non\u2212Coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, DK-1870 Frederiksberg, Denmark and 6The Santa Fe Institute, Santa Fe, 87501 NM, USA"},{"name":"1 Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria, 2Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, 3Max Planck Institute for Mathematics in the Sciences, 4RNomics Group, Fraunhofer IZI, D-04103 Leipzig, Germany, 5Center for Non\u2212Coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, DK-1870 Frederiksberg, Denmark and 6The Santa Fe Institute, Santa Fe, 87501 NM, USA"},{"name":"1 Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria, 2Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, 3Max Planck Institute for Mathematics in the Sciences, 4RNomics Group, Fraunhofer IZI, D-04103 Leipzig, Germany, 5Center for Non\u2212Coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, DK-1870 Frederiksberg, Denmark and 6The Santa Fe Institute, Santa Fe, 87501 NM, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ivo L.","family":"Hofacker","sequence":"additional","affiliation":[{"name":"1 Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria, 2Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, 3Max Planck Institute for Mathematics in the Sciences, 4RNomics Group, Fraunhofer IZI, D-04103 Leipzig, Germany, 5Center for Non\u2212Coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, DK-1870 Frederiksberg, Denmark and 6The Santa Fe Institute, Santa Fe, 87501 NM, USA"},{"name":"1 Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria, 2Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, 3Max Planck Institute for Mathematics in the Sciences, 4RNomics Group, Fraunhofer IZI, D-04103 Leipzig, Germany, 5Center for Non\u2212Coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, DK-1870 Frederiksberg, Denmark and 6The Santa Fe Institute, Santa Fe, 87501 NM, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,6,14]]},"reference":[{"key":"2023012512015596700_B1","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/j.jmb.2003.12.041","article-title":"A new algorithm for RNA secondary structure design","volume":"336","author":"Andronescu","year":"2004","journal-title":"J. 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