{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T20:53:30Z","timestamp":1782939210886,"version":"3.54.5"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2019,4,26]],"date-time":"2019-04-26T00:00:00Z","timestamp":1556236800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31600592"],"award-info":[{"award-number":["31600592"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["GM083107"],"award-info":[{"award-number":["GM083107"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["GM116960"],"award-info":[{"award-number":["GM116960"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AI134678"],"award-info":[{"award-number":["AI134678"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI1564756"],"award-info":[{"award-number":["DBI1564756"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Extreme Science and Engineering Discovery Environment"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Comparison of RNA 3D structures can be used to infer functional relationship of RNA molecules. Most of the current RNA structure alignment programs are built on size-dependent scales, which complicate the interpretation of structure and functional relations. Meanwhile, the low speed prevents the programs from being applied to large-scale RNA structural database search.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed an open-source algorithm, RNA-align, for RNA 3D structure alignment which has the structure similarity scaled by a size-independent and statistically interpretable scoring metric. Large-scale benchmark tests show that RNA-align significantly outperforms other state-of-the-art programs in both alignment accuracy and running speed. The major advantage of RNA-align lies at the quick convergence of the heuristic alignment iterations and the coarse-grained secondary structure assignment, both of which are crucial to the speed and accuracy of RNA structure alignments.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/zhanglab.ccmb.med.umich.edu\/RNA-align\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz282","type":"journal-article","created":{"date-parts":[[2019,4,18]],"date-time":"2019-04-18T11:24:23Z","timestamp":1555586663000},"page":"4459-4461","source":"Crossref","is-referenced-by-count":103,"title":["RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA"],"prefix":"10.1093","volume":"35","author":[{"given":"Sha","family":"Gong","sequence":"first","affiliation":[{"name":"School of Physics and Electronic Information, Huanggang Normal University , Huanggang, China"},{"name":"Department of Computational Medicine and Bioinformatics , Ann Arbor, MI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7290-1324","authenticated-orcid":false,"given":"Chengxin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics , Ann Arbor, MI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics , Ann Arbor, MI, USA"},{"name":"Department of Biological Chemistry, University of Michigan , Ann Arbor, MI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,4,25]]},"reference":[{"key":"2023062803480495300_btz282-B1","doi-asserted-by":"crossref","first-page":"I112","DOI":"10.1093\/bioinformatics\/btn288","article-title":"RNA structure alignment by a unit-vector approach","volume":"24","author":"Capriotti","year":"2008","journal-title":"Bioinformatics"},{"key":"2023062803480495300_btz282-B2","doi-asserted-by":"crossref","first-page":"W412","DOI":"10.1093\/nar\/gkl312","article-title":"The ARTS web server for aligning RNA tertiary structures","volume":"34","author":"Dror","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023062803480495300_btz282-B3","article-title":"STAR3D: a stack-based RNA 3D structural alignment tool","volume":"43","author":"Ge","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023062803480495300_btz282-B4","doi-asserted-by":"crossref","DOI":"10.1063\/1.4927390","article-title":"The regulation mechanism of yitJ and metF riboswitches","volume":"143","author":"Gong","year":"2015","journal-title":"J. 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