{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T20:44:45Z","timestamp":1776804285452,"version":"3.51.2"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Three-dimensional RNA structure prediction and folding is of significant interest in the biological research community. Here, we present iFoldRNA, a novel web-based methodology for RNA structure prediction with near atomic resolution accuracy and analysis of RNA folding thermodynamics. iFoldRNA rapidly explores RNA conformations using discrete molecular dynamics simulations of input RNA sequences. Starting from simplified linear-chain conformations, RNA molecules (&amp;lt;50 nt) fold to native-like structures within half an hour of simulation, facilitating rapid RNA structure prediction. All-atom reconstruction of energetically stable conformations generates iFoldRNA predicted RNA structures. The predicted RNA structures are within 2\u20135 \u00c5 root mean squre deviations (RMSDs) from corresponding experimentally derived structures. RNA folding parameters including specific heat, contact maps, simulation trajectories, gyration radii, RMSDs from native state, fraction of native-like contacts are accessible from iFoldRNA. We expect iFoldRNA will serve as a useful resource for RNA structure prediction and folding thermodynamic analyses.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/iFoldRNA.dokhlab.org.<\/jats:p>\n               <jats:p>Contact: \u00a0dokh@med.unc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn328","type":"journal-article","created":{"date-parts":[[2008,6,26]],"date-time":"2008-06-26T00:44:20Z","timestamp":1214441060000},"page":"1951-1952","source":"Crossref","is-referenced-by-count":223,"title":["iFoldRNA: three-dimensional RNA structure prediction and folding"],"prefix":"10.1093","volume":"24","author":[{"given":"Shantanu","family":"Sharma","sequence":"first","affiliation":[{"name":"Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Feng","family":"Ding","sequence":"additional","affiliation":[{"name":"Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nikolay V.","family":"Dokholyan","sequence":"additional","affiliation":[{"name":"Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,6,25]]},"reference":[{"key":"2023020211092340400_B1","doi-asserted-by":"crossref","first-page":"14664","DOI":"10.1073\/pnas.0703836104","article-title":"Automated de novo prediction of native-like RNA tertiary structures.","volume":"104","author":"Das","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020211092340400_B2","doi-asserted-by":"crossref","first-page":"e85","DOI":"10.1371\/journal.pcbi.0020085","article-title":"Emergence of protein fold families through rational design.","volume":"2","author":"Ding","year":"2006","journal-title":"PLoS. Comput. Biol."},{"key":"2023020211092340400_B3","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":"2023020211092340400_B4","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":"2023020211092340400_B5","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/nature06684","article-title":"The MC-fold and MC-sym pipeline infers RNA structure from sequence data.","volume":"452","author":"Parisien","year":"2008","journal-title":"Nature"},{"key":"2023020211092340400_B6","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/j.sbi.2007.03.001","article-title":"Bridging the gap in RNA structure prediction.","volume":"17","author":"Shapiro","year":"2007","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2023020211092340400_B7","doi-asserted-by":"crossref","first-page":"2693","DOI":"10.1093\/bioinformatics\/btl460","article-title":"iFold: a platform for interactive folding simulations of proteins.","volume":"22","author":"Sharma","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020211092340400_B8","doi-asserted-by":"crossref","first-page":"4659","DOI":"10.1021\/ja0436749","article-title":"RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts.","volume":"127","author":"Wilkinson","year":"2005","journal-title":"J. Am. Chem. Soc."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/17\/1951\/49050848\/bioinformatics_24_17_1951.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/17\/1951\/49050848\/bioinformatics_24_17_1951.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T13:09:03Z","timestamp":1675343343000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/17\/1951\/261371"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,6,25]]},"references-count":8,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2008,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn328","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,9,1]]},"published":{"date-parts":[[2008,6,25]]}}}