{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,5]],"date-time":"2025-04-05T07:44:57Z","timestamp":1743839097632},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: To gain insight into how biopolymers fold as quickly as they do, it is useful to determine which structural elements limit the rate of RNA\/protein folding.<\/jats:p>\n               <jats:p>Summary: We have created a new web server, FoldNucleus. Using this server, it is possible to calculate the folding nucleus for RNA molecules with known 3D structures\u2014including pseudoknots, tRNAs, hairpins and ribozymes\u2014and for protein molecules with known 3D structures, as long as they are smaller than 200 amino acid residues. Researchers can determine and understand which elements of the structure limit the folding process for various types of RNAs and protein molecules. Experimental \u0424 values for 21 proteins can be found and compared with those determined by our method: http:\/\/bioinfo.protres.ru\/resources\/phi_values.htm.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0http:\/\/bioinfo.protres.ru\/foldnucleus\/.<\/jats:p>\n               <jats:p>Contact: \u00a0ogalzit@vega.protres.ru<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv369","type":"journal-article","created":{"date-parts":[[2015,6,24]],"date-time":"2015-06-24T00:00:24Z","timestamp":1435104024000},"page":"3374-3376","source":"Crossref","is-referenced-by-count":5,"title":["FoldNucleus: web server for the prediction of RNA and protein folding nuclei from their 3D structures"],"prefix":"10.1093","volume":"31","author":[{"given":"Leonid B.","family":"Pereyaslavets","sequence":"first","affiliation":[{"name":"Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia"}]},{"given":"Igor V.","family":"Sokolovsky","sequence":"additional","affiliation":[{"name":"Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia"}]},{"given":"Oxana V.","family":"Galzitskaya","sequence":"additional","affiliation":[{"name":"Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia"}]}],"member":"286","published-online":{"date-parts":[[2015,6,22]]},"reference":[{"key":"2023020202320548500_btv369-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":"2023020202320548500_btv369-B2","doi-asserted-by":"crossref","first-page":"11299","DOI":"10.1073\/pnas.96.20.11299","article-title":"A theoretical search for folding\/unfolding nuclei in three-dimensional protein structures","volume":"96","author":"Galzitskaya","year":"1999","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020202320548500_btv369-B3","first-page":"44","article-title":"Are there pathways for protein folding?","volume":"65","author":"Levinthal","year":"1968","journal-title":"J. Chem. Phys."},{"key":"2023020202320548500_btv369-B4","doi-asserted-by":"crossref","first-page":"7461","DOI":"10.1021\/ja9913075","article-title":"Probing the structure of an RNA tertiary unfolding transition state","volume":"121","author":"Maglott","year":"1999","journal-title":"J. Am. Chem. Soc."},{"key":"2023020202320548500_btv369-B5","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1038\/346440a0","article-title":"Transient folding intermediates characterized by protein engineering","volume":"346","author":"Matouschek","year":"1990","journal-title":"Nature"},{"key":"2023020202320548500_btv369-B6","first-page":"236","article-title":"Prediction of folding nuclei in tRNA molecules","volume":"76","author":"Pereyaslavets","year":"2011","journal-title":"Biochemistry"},{"key":"2023020202320548500_btv369-B7","doi-asserted-by":"crossref","first-page":"4957","DOI":"10.1021\/bi047314+","article-title":"RNA and protein folding: common themes and variations","volume":"44","author":"Thirumalai","year":"2005","journal-title":"Biochemistry"},{"key":"2023020202320548500_btv369-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\/31\/20\/3374\/49036163\/bioinformatics_31_20_3374.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/20\/3374\/49036163\/bioinformatics_31_20_3374.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T03:50:24Z","timestamp":1675309824000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/20\/3374\/195897"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,6,22]]},"references-count":8,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2015,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv369","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,10,15]]},"published":{"date-parts":[[2015,6,22]]}}}