{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,14]],"date-time":"2026-06-14T08:47:46Z","timestamp":1781426866938,"version":"3.54.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,10,12]],"date-time":"2016-10-12T00:00:00Z","timestamp":1476230400000},"content-version":"vor","delay-in-days":399,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Summary: Chemical mapping experiments allow for nucleotide resolution assessment of RNA structure. We demonstrate that different strategies of integrating probing data with thermodynamics-based RNA secondary structure prediction algorithms can be implemented by means of soft constraints. This amounts to incorporating suitable pseudo-energies into the standard energy model for RNA secondary structures. As a showcase application for this new feature of the ViennaRNA Package we compare three distinct, previously published strategies to utilize SHAPE reactivities for structure prediction. The new tool is benchmarked on a set of RNAs with known reference structure.<\/jats:p>\n                  <jats:p>Availability and implementation: The capability for SHAPE directed RNA folding is part of the upcoming release of the ViennaRNA Package 2.2, for which a preliminary release is already freely available at http:\/\/www.tbi.univie.ac.at\/RNA.<\/jats:p>\n                  <jats:p>Contact: michael.wolfinger@univie.ac.at<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv523","type":"journal-article","created":{"date-parts":[[2015,9,10]],"date-time":"2015-09-10T09:37:06Z","timestamp":1441877826000},"page":"145-147","source":"Crossref","is-referenced-by-count":98,"title":["SHAPE directed RNA folding"],"prefix":"10.1093","volume":"32","author":[{"given":"Ronny","family":"Lorenz","sequence":"first","affiliation":[{"name":"2 \u00a01Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria,"},{"name":"2 \u00a01Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dominik","family":"Luntzer","sequence":"additional","affiliation":[{"name":"2 \u00a01Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivo L.","family":"Hofacker","sequence":"additional","affiliation":[{"name":"2 \u00a01Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria,"},{"name":"2 \u00a01Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter F.","family":"Stadler","sequence":"additional","affiliation":[{"name":"2 \u00a01Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria,"},{"name":"2 \u00a01Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael T.","family":"Wolfinger","sequence":"additional","affiliation":[{"name":"2 \u00a01Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria,"},{"name":"2 \u00a01Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria,"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,9,9]]},"reference":[{"key":"2023020110212644800_btv523-B1","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1073\/pnas.0806929106","article-title":"Accurate SHAPE-directed RNA structure determination","volume":"106","author":"Deigan","year":"2009","journal-title":"PNAS"},{"key":"2023020110212644800_btv523-B2","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1146\/annurev-biophys-051013-022950","article-title":"Computational analysis of conserved RNA secondary structure in transcriptomes and genomes","volume":"43","author":"Eddy","year":"2014","journal-title":"Annu. Rev. Biophys."},{"key":"2023020110212644800_btv523-B3","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1093\/nar\/gkn188","article-title":"The Vienna RNA websuite","volume":"36","author":"Gruber","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023020110212644800_btv523-B4","doi-asserted-by":"crossref","first-page":"5498","DOI":"10.1073\/pnas.1219988110","article-title":"Accurate SHAPE-directed RNA secondary structure modelling, including pseudoknots","volume":"110","author":"Hajdin","year":"2013","journal-title":"Proc. Natl Acad. 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