{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:42:38Z","timestamp":1753875758829,"version":"3.41.2"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2024,11,15]],"date-time":"2024-11-15T00:00:00Z","timestamp":1731628800000},"content-version":"vor","delay-in-days":14,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01GM085328"],"award-info":[{"award-number":["R01GM085328"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The recent progress in RNA structure determination methods has resulted in a surge of newly solved RNA 3D structures. However, there is an absence of a user-friendly browser-based tool that can facilitate the comparison and visualization of RNA motifs across multiple 3D structures.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We introduce R3DMCS, a web server that allows users to compare selected RNA nucleotides across all 3D structures of a given molecule from a given species, or across all 3D structures mapped to a single Rfam family. Starting from one instance of the motif, R3DMCS retrieves, aligns, annotates, organizes, and displays 3D coordinates of corresponding sets of nucleotides from other 3D structures. With R3DMCS, one can explore conformational changes of motifs due to 3D structures being solved in different functional states or different experimental conditions. One can also investigate conservation of 3D structure across species, or changes in 3D structure due to changes in sequence.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>R3DMCS is open-source software and freely available at https:\/\/rna.bgsu.edu\/correspondence\/ and https:\/\/github.com\/BGSU-RNA\/RNA-3D-correspondence.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae682","type":"journal-article","created":{"date-parts":[[2024,11,15]],"date-time":"2024-11-15T17:05:22Z","timestamp":1731690322000},"source":"Crossref","is-referenced-by-count":0,"title":["R3DMCS: a web server for visualizing structural variation in RNA motifs across experimental 3D structures from the same organism or across species"],"prefix":"10.1093","volume":"40","author":[{"given":"Sri Devan","family":"Appasamy","sequence":"first","affiliation":[{"name":"Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridge CB10 1SD,","place":["United Kingdom"]},{"name":"Department of Biological Sciences, Bowling Green State University , Bowling Green, OH 43403,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3281-918X","authenticated-orcid":false,"given":"Craig L","family":"Zirbel","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, Bowling Green State University , Bowling Green, OH 43403,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2024,11,15]]},"reference":[{"key":"2024112518322465000_btae682-B1","doi-asserted-by":"crossref","first-page":"D266","DOI":"10.1093\/nar\/gkv1186","article-title":"InterRNA: a database of base interactions in RNA structures","volume":"44","author":"Appasamy","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2024112518322465000_btae682-B2","doi-asserted-by":"crossref","first-page":"D123","DOI":"10.1093\/nar\/gkt1084","article-title":"RNA bricks\u2014a database of RNA 3D motifs and their interactions","volume":"42","author":"Chojnowski","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2024112518322465000_btae682-B3","doi-asserted-by":"crossref","first-page":"8188","DOI":"10.1073\/pnas.1605127113","article-title":"Resistance mutations generate divergent antibiotic susceptibility profiles against translation inhibitors","volume":"113","author":"Cocozaki","year":"2016","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024112518322465000_btae682-B4","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1038\/s41580-019-0136-0","article-title":"The roles of structural dynamics in the cellular functions of RNAs","volume":"20","author":"Ganser","year":"2019","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2024112518322465000_btae682-B5","doi-asserted-by":"crossref","first-page":"4784","DOI":"10.1038\/s41467-023-40422-7","article-title":"Modulation of translational decoding by m6A modification of mRNA","volume":"14","author":"Jain","year":"2023","journal-title":"Nat Commun"},{"key":"2024112518322465000_btae682-B6","doi-asserted-by":"crossref","first-page":"D192","DOI":"10.1093\/nar\/gkaa1047","article-title":"Rfam 14: expanded coverage of metagenomic, viral and microRNA families","volume":"49","author":"Kalvari","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2024112518322465000_btae682-B7","doi-asserted-by":"crossref","first-page":"D245","DOI":"10.1093\/nar\/gkad957","article-title":"The nucleic acid knowledgebase: a new portal for 3D structural information about nucleic acids","volume":"52","author":"Lawson","year":"2024","journal-title":"Nucleic Acids 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motifs and the RNA 3D Motif Atlas","volume":"19","author":"Petrov","year":"2013","journal-title":"RNA"},{"key":"2024112518322465000_btae682-B12","doi-asserted-by":"crossref","first-page":"baz153","DOI":"10.1093\/database\/baz153","article-title":"RNA CoSSMos 2.0: an improved searchable database of secondary structure motifs in RNA three-dimensional structures","volume":"2020","author":"Richardson","year":"2020","journal-title":"Database"},{"key":"2024112518322465000_btae682-B13","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1007\/s00285-007-0110-x","article-title":"FR3D: finding local and composite recurrent structural motifs in RNA 3D structures","volume":"56","author":"Sarver","year":"2008","journal-title":"J Math Biol"},{"key":"2024112518322465000_btae682-B14","doi-asserted-by":"crossref","first-page":"5517","DOI":"10.1016\/j.cell.2023.10.026","article-title":"Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic 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