{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T20:07:16Z","timestamp":1778011636844,"version":"3.51.4"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: RNA molecules play important roles in key biological processes in the cell and are becoming attractive for developing therapeutic applications. Since the function of RNA depends on its structure and dynamics, comparing and classifying the RNA 3D structures is of crucial importance to molecular biology. In this study, we have developed Rclick, a web server that is capable of superimposing RNA 3D structures by using clique matching and 3D least-squares fitting. Our server Rclick has been benchmarked and compared with other popular servers and methods for RNA structural alignments. In most cases, Rclick alignments were better in terms of structure overlap. Our server also recognizes conformational changes between structures. For this purpose, the server produces complementary alignments to maximize the extent of detectable similarity. Various examples showcase the utility of our web server for comparison of RNA, RNA\u2013protein complexes and RNA-ligand structures.<\/jats:p>\n               <jats:p>Availability and implementation: The Rclick web server is freely accessible at http:\/\/mspc.bii.a-star.edu.sg\/minhn\/rclick.html<\/jats:p>\n               <jats:p>Contact: \u00a0minhn@bii.a-star.edu.sg<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu752","type":"journal-article","created":{"date-parts":[[2014,11,13]],"date-time":"2014-11-13T05:02:10Z","timestamp":1415854930000},"page":"966-968","source":"Crossref","is-referenced-by-count":23,"title":["Rclick: a web server for comparison of RNA 3D structures"],"prefix":"10.1093","volume":"31","author":[{"given":"Minh N.","family":"Nguyen","sequence":"first","affiliation":[{"name":"1 Biomolecular Modeling and Design Division, Singapore 138671 Singapore, 2Department of Biological Sciences, National University of Singapore, Singapore and 3School of Biological Sciences, Nanyang Technological University, Singapore, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chandra","family":"Verma","sequence":"additional","affiliation":[{"name":"1 Biomolecular Modeling and Design Division, Singapore 138671 Singapore, 2Department of Biological Sciences, National University of Singapore, Singapore and 3School of Biological Sciences, Nanyang Technological University, Singapore, Singapore"},{"name":"1 Biomolecular Modeling and Design Division, Singapore 138671 Singapore, 2Department of Biological Sciences, National University of Singapore, Singapore and 3School of Biological Sciences, Nanyang Technological University, Singapore, Singapore"},{"name":"1 Biomolecular Modeling and Design Division, Singapore 138671 Singapore, 2Department of Biological Sciences, National University of Singapore, Singapore and 3School of Biological Sciences, Nanyang Technological University, Singapore, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,11,12]]},"reference":[{"key":"2023020116180015700_btu752-B1","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023020116180015700_btu752-B2","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":"2023020116180015700_btu752-B3","doi-asserted-by":"crossref","first-page":"W260","DOI":"10.1093\/nar\/gkp433","article-title":"SARA: a server for function annotation of RNA structures","volume":"37","author":"Capriotti","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023020116180015700_btu752-B4","doi-asserted-by":"crossref","first-page":"W42","DOI":"10.1093\/nar\/gks560","article-title":"SETTER: web server for RNA structure comparison","volume":"40","author":"Cech","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023020116180015700_btu752-B5","doi-asserted-by":"crossref","first-page":"D310","DOI":"10.1093\/nar\/gkn877","article-title":"The CATH classification revisited-architectures reviewed and new ways to characterize structural divergence in superfamilies","volume":"37","author":"Cuff","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023020116180015700_btu752-B6","doi-asserted-by":"crossref","first-page":"ii47","DOI":"10.1093\/bioinformatics\/bti1108","article-title":"ARTS: alignment of RNA tertiary structures","volume":"21","author":"Dror","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020116180015700_btu752-B7","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":"2023020116180015700_btu752-B8","doi-asserted-by":"crossref","first-page":"1858","DOI":"10.1093\/bioinformatics\/bts301","article-title":"Efficient RNA pairwise structure comparison by SETTER method","volume":"28","author":"Hoksza","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020116180015700_btu752-B9","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.1016\/j.jmb.2004.12.032","article-title":"Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures","volume":"346","author":"Kolodny","year":"2005","journal-title":"J. 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