{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,28]],"date-time":"2025-11-28T17:11:03Z","timestamp":1764349863208},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: RNA atomic resolution structures have revealed the existance of different families of basepair interactions, each of which with its own isosteric sub-families. Ribostral (Ribonucleic Structural Aligner) is a user-friendly framework for analyzing, evaluating and viewing RNA sequence alignments with at least one available atomic resolution structure. It is the first of its kind that makes direct and easy- to-understand superposition of the isostericity matrices of basepairs observed in the structure onto sequence alignments, easily indicating allowed and unallowed substitutions at each BP position. Potential mistakes in the alignments can then be corrected using other sequence editing software. Ribostral has been developed and tested under Windows XP, and is capable of running on any PC or MAC platform with MATLAB 7.1 (SP3) or higher installed version. A stand-alone version is also available for the PC platform.<\/jats:p>\n               <jats:p>Availability: \u00a0<\/jats:p>\n               <jats:p>Contact: \u00a0mali@bgsu.edu<\/jats:p>\n               <jats:p>Supplementary information: A user manual is available on Ribostral website.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl360","type":"journal-article","created":{"date-parts":[[2006,7,6]],"date-time":"2006-07-06T01:54:39Z","timestamp":1152150879000},"page":"2168-2170","source":"Crossref","is-referenced-by-count":12,"title":["Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities"],"prefix":"10.1093","volume":"22","author":[{"given":"Ali","family":"Mokdad","sequence":"first","affiliation":[{"name":"Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University \u00a0 OH 43403, USA"}]},{"given":"Neocles B.","family":"Leontis","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University \u00a0 OH 43403, USA"}]}],"member":"286","published-online":{"date-parts":[[2006,7,4]]},"reference":[{"key":"2023012409133807000_b1","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1126\/science.289.5481.905","article-title":"The complete atomic structure of the large ribosomal subunit at 2.4 A resolution","volume":"289","author":"Ban","year":"2000","journal-title":"Science"},{"key":"2023012409133807000_b2","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1093\/nar\/gkg006","article-title":"Rfam: an RNA family database","volume":"31","author":"Griffiths-Jones","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012409133807000_b3","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":"2023012409133807000_b4","doi-asserted-by":"crossref","first-page":"3497","DOI":"10.1093\/nar\/gkf481","article-title":"The non-Watson\u2013Crick base pairs and their associated isostericity matrices","volume":"30","author":"Leontis","year":"2002","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/17\/2168\/48839980\/bioinformatics_22_17_2168.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/17\/2168\/48839980\/bioinformatics_22_17_2168.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T09:21:24Z","timestamp":1674552084000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/17\/2168\/274762"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,7,4]]},"references-count":4,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2006,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl360","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,9,1]]},"published":{"date-parts":[[2006,7,4]]}}}