{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T00:55:26Z","timestamp":1675299326808},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2016,10,4]],"date-time":"2016-10-04T00:00:00Z","timestamp":1475539200000},"content-version":"vor","delay-in-days":1225,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,7,1]]},"DOI":"10.1093\/nar\/gkt417","type":"journal-article","created":{"date-parts":[[2013,5,29]],"date-time":"2013-05-29T00:37:24Z","timestamp":1369787844000},"page":"W15-W21","source":"Crossref","is-referenced-by-count":12,"title":["R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures"],"prefix":"10.1093","volume":"41","author":[{"given":"Ryan R.","family":"Rahrig","sequence":"first","affiliation":[]},{"given":"Anton I.","family":"Petrov","sequence":"additional","affiliation":[]},{"given":"Neocles B.","family":"Leontis","sequence":"additional","affiliation":[]},{"given":"Craig L.","family":"Zirbel","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2013,5,28]]},"reference":[{"key":"key\n\t\t\t\t20171013125909_gkt417-B1","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/0092-8674(86)90315-6","article-title":"Ribosomal RNA phylogeny and the primary lines of evolutionary descent","volume":"45","author":"Pace","year":"1986","journal-title":"Cell"},{"key":"key\n\t\t\t\t20171013125909_gkt417-B2","doi-asserted-by":"crossref","first-page":"1623","DOI":"10.1261\/rna.1601409","article-title":"The RNA structure alignment ontology","volume":"15","author":"Brown","year":"2009","journal-title":"RNA"},{"key":"key\n\t\t\t\t20171013125909_gkt417-B3","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1016\/S0076-6879(00)17031-4","article-title":"Modeling RNA tertiary structure from patterns of sequence variation","volume":"317","author":"Michel","year":"2000","journal-title":"Methods Enzymol."},{"key":"key\n\t\t\t\t20171013125909_gkt417-B4","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1016\/j.sbi.2006.04.004","article-title":"Multiple sequence alignment","volume":"16","author":"Edgar","year":"2006","journal-title":"Curr. Opin. Struct. Biol."},{"key":"key\n\t\t\t\t20171013125909_gkt417-B5","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","article-title":"A general method applicable to the search for similarities in the amino acid sequence of two proteins","volume":"48","author":"Needleman","year":"1970","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20171013125909_gkt417-B6","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1073\/pnas.69.1.4","article-title":"Matching sequences under deletion-insertion constraints","volume":"69","author":"Sankoff","year":"1972","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20171013125909_gkt417-B7","volume-title":"Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids","author":"Durbin","year":"1998"},{"key":"key\n\t\t\t\t20171013125909_gkt417-B8","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":"key\n\t\t\t\t20171013125909_gkt417-B9","doi-asserted-by":"crossref","first-page":"W659","DOI":"10.1093\/nar\/gkm334","article-title":"DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities","volume":"35","author":"Ferr\u00e8","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013125909_gkt417-B10","doi-asserted-by":"crossref","first-page":"W19","DOI":"10.1093\/nar\/gkn327","article-title":"SARSA: a web tool for structural alignment of RNA using a structural alphabet","volume":"36","author":"Chang","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013125909_gkt417-B11","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":"key\n\t\t\t\t20171013125909_gkt417-B12","doi-asserted-by":"crossref","first-page":"692","DOI":"10.3390\/a2020692","article-title":"Fast structural alignment of biomolecules using a hash table, n-grams and string descriptors","volume":"2","author":"Bauer","year":"2009","journal-title":"Algorithms"},{"key":"key\n\t\t\t\t20171013125909_gkt417-B13","doi-asserted-by":"crossref","first-page":"2689","DOI":"10.1093\/bioinformatics\/btq506","article-title":"R3D Align: global pairwise alignment of RNA 3D structures using local superpositions","volume":"26","author":"Rahrig","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013125909_gkt417-B14","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":"key\n\t\t\t\t20171013125909_gkt417-B15","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":"key\n\t\t\t\t20171013125909_gkt417-B16","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":"key\n\t\t\t\t20171013125909_gkt417-B17","doi-asserted-by":"crossref","first-page":"W340","DOI":"10.1093\/nar\/gkq483","article-title":"iPARTS: an improved tool of pairwise alignment of RNA tertiary structures","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013125909_gkt417-B18","doi-asserted-by":"crossref","first-page":"W42","DOI":"10.1093\/nar\/gks560","article-title":"SETTER: web server for RNA structure comparison","volume":"40","author":"\u010cech","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013125909_gkt417-B19","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":"key\n\t\t\t\t20171013125909_gkt417-B20","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":"key\n\t\t\t\t20171013125909_gkt417-B21","article-title":"Nonredundant 3D Structure Datasets for RNA knowledge extraction and benchmarking","volume-title":"RNA 3D Structure Analysis and Prediction","author":"Leontis","year":"2012"},{"key":"key\n\t\t\t\t20171013125909_gkt417-B22","article-title":"Color universal design: the selection of four easily distinguishable colors for all color vision types","author":"Ichihara","year":"2008"},{"key":"key\n\t\t\t\t20171013125909_gkt417-B23","doi-asserted-by":"crossref","first-page":"W50","DOI":"10.1093\/nar\/gkr249","article-title":"WebFR3D\u2013a server for finding, aligning and analyzing recurrent RNA 3D motifs","volume":"39","author":"Petrov","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013125909_gkt417-B24","doi-asserted-by":"crossref","first-page":"e95","DOI":"10.1093\/nar\/gks241","article-title":"R-CHIE: a web server and R package for visualizing RNA secondary structures","volume":"40","author":"Lai","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013125909_gkt417-B25","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1261\/rna.033365.112","article-title":"Visualizing RNA base-pairing probabilities with RNAbow diagrams","volume":"19","author":"Aalberts","year":"2013","journal-title":"RNA"},{"key":"key\n\t\t\t\t20171013125909_gkt417-B26","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1017\/S1355838201002515","article-title":"Geometric nomenclature and classification of RNA base pairs","volume":"7","author":"Leontis","year":"2001","journal-title":"RNA"},{"key":"key\n\t\t\t\t20171013125909_gkt417-B27","doi-asserted-by":"crossref","first-page":"2294","DOI":"10.1093\/nar\/gkp011","article-title":"Frequency and isostericity of RNA base pairs","volume":"37","author":"Stombaugh","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013125909_gkt417-B28","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1261\/rna.031054.111","article-title":"RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction","volume":"18","author":"Cruz","year":"2012","journal-title":"RNA"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/41\/W1\/W15\/16943162\/gkt417.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T10:41:18Z","timestamp":1522665678000},"score":1,"resource":{"primary":{"URL":"http:\/\/academic.oup.com\/nar\/article\/41\/W1\/W15\/1103501\/R3D-Align-web-server-for-global-nucleotide-to"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,5,28]]},"references-count":28,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2013,5,28]]},"published-print":{"date-parts":[[2013,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkt417","relation":{},"ISSN":["1362-4962","0305-1048"],"issn-type":[{"value":"1362-4962","type":"electronic"},{"value":"0305-1048","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,7,1]]},"published":{"date-parts":[[2013,5,28]]}}}