{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T03:47:57Z","timestamp":1781754477032,"version":"3.54.5"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: A key to understanding RNA function is to uncover its complex 3D structure. Experimental methods used for determining RNA 3D structures are technologically challenging and laborious, which makes the development of computational prediction methods of substantial interest. Previously, we developed the iFoldRNA server that allows accurate prediction of short (&amp;lt;50\u2009nt) tertiary RNA structures starting from primary sequences. Here, we present a new version of the iFoldRNA server that permits the prediction of tertiary structure of RNAs as long as a few hundred nucleotides. This substantial increase in the server capacity is achieved by utilization of experimental information such as base-pairing and hydroxyl-radical probing. We demonstrate a significant benefit provided by integration of experimental data and computational methods.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0http:\/\/ifoldrna.dokhlab.org<\/jats:p>\n               <jats:p>Contact: \u00a0dokh@unc.eu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv221","type":"journal-article","created":{"date-parts":[[2015,4,25]],"date-time":"2015-04-25T01:51:42Z","timestamp":1429926702000},"page":"2891-2893","source":"Crossref","is-referenced-by-count":127,"title":["iFoldRNA v2: folding RNA with constraints"],"prefix":"10.1093","volume":"31","author":[{"given":"Andrey","family":"Krokhotin","sequence":"first","affiliation":[{"name":"Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin","family":"Houlihan","sequence":"additional","affiliation":[{"name":"Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nikolay V.","family":"Dokholyan","sequence":"additional","affiliation":[{"name":"Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,4,24]]},"reference":[{"key":"2023020202203316400_btv221-B1","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1261\/rna.894608","article-title":"Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms","volume":"14","author":"Ding","year":"2008","journal-title":"RNA"},{"key":"2023020202203316400_btv221-B2","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nmeth.1976","article-title":"Three-dimensional RNA structure refinement by hydroxyl radical probing","volume":"9","author":"Ding","year":"2012","journal-title":"Nat. Methods"},{"key":"2023020202203316400_btv221-B3","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1016\/S1359-0278(98)00072-8","article-title":"Discrete molecular dynamics studies of the folding of a protein-like model","volume":"3","author":"Dokholyan","year":"1998","journal-title":"Fold. Des."},{"key":"2023020202203316400_btv221-B4","doi-asserted-by":"crossref","first-page":"1340","DOI":"10.1261\/rna.1837410","article-title":"On the significance of an RNA tertiary structure prediction","volume":"16","author":"Hajdin","year":"2010","journal-title":"RNA"},{"key":"2023020202203316400_btv221-B5","doi-asserted-by":"crossref","first-page":"13858","DOI":"10.1073\/pnas.1407306111","article-title":"Single-molecule correlated chemical probing of RNA","volume":"111","author":"Homan","year":"2014","journal-title":"Proc. Natl Acad. Sci. U.S.A."},{"key":"2023020202203316400_btv221-B6","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1006\/jmbi.2001.4626","article-title":"Quantitative analysis of nucleic acid three-dimensional structures","volume":"308","author":"Gendron","year":"2001","journal-title":"J. Mol. Biol."},{"key":"2023020202203316400_btv221-B7","doi-asserted-by":"crossref","first-page":"2541","DOI":"10.1021\/ja805460e","article-title":"Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics","volume":"131","author":"Gherghe","year":"2009","journal-title":"J. Am. Chem. Soc."},{"key":"2023020202203316400_btv221-B8","doi-asserted-by":"crossref","first-page":"5785","DOI":"10.1093\/nar\/20.21.5785","article-title":"Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods","volume":"20","author":"Gutell","year":"1992","journal-title":"Nucleic Acids Res."},{"key":"2023020202203316400_btv221-B9","doi-asserted-by":"crossref","first-page":"4931","DOI":"10.1021\/bi100142y","article-title":"Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain","volume":"49","author":"Lavender","year":"2010","journal-title":"Biochemistry"},{"key":"2023020202203316400_btv221-B10","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1016\/j.ymeth.2010.06.007","article-title":"SHAPE-directed RNA secondary structure prediction","volume":"52","author":"Low","year":"2010","journal-title":"Methods"},{"key":"2023020202203316400_btv221-B11","doi-asserted-by":"crossref","first-page":"1875","DOI":"10.1261\/rna.1700409","article-title":"New metrics for comparing and assessing discrepancies between RNA 3D structures and models","volume":"15","author":"Parisien","year":"2009","journal-title":"RNA"},{"key":"2023020202203316400_btv221-B12","doi-asserted-by":"crossref","first-page":"e112","DOI":"10.1093\/nar\/gks339","article-title":"Automated 3D structure composition for large RNAs","volume":"40","author":"Popenda","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023020202203316400_btv221-B13","doi-asserted-by":"crossref","first-page":"1951","DOI":"10.1093\/bioinformatics\/btn328","article-title":"iFoldRNA: three-dimensional RNA structure prediction and folding","volume":"22","author":"Sharma","year":"2008","journal-title":"Bioinformatics"},{"key":"2023020202203316400_btv221-B14","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/S0009-2614(99)01123-9","article-title":"Replica-exchange molecular dynamics method for protein folding","volume":"314","author":"Sugita","year":"1999","journal-title":"Chem. Phys. Lett."},{"key":"2023020202203316400_btv221-B15","doi-asserted-by":"crossref","DOI":"10.1038\/srep00734","article-title":"Automated and fast building of three-dimensional RNA structures","volume":"2","author":"Zhao","year":"2012","journal-title":"Sci. Rep."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/17\/2891\/49034850\/bioinformatics_31_17_2891.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/17\/2891\/49034850\/bioinformatics_31_17_2891.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T03:44:29Z","timestamp":1675309469000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/17\/2891\/182977"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,4,24]]},"references-count":15,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2015,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv221","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,9,1]]},"published":{"date-parts":[[2015,4,24]]}}}