{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T10:36:05Z","timestamp":1784889365461,"version":"3.55.0"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: RBSDesigner predicts the translation efficiency of existing mRNA sequences and designs synthetic ribosome binding sites (RBSs) for a given coding sequence (CDS) to yield a desired level of protein expression. The program implements the mathematical model for translation initiation described in Na et al. (Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with a desired expression level in prokaryotes. BMC Syst. Biol., 4, 71). The program additionally incorporates the effect on translation efficiency of the spacer length between a Shine\u2013Dalgarno (SD) sequence and an AUG codon, which is crucial for the incorporation of fMet-tRNA into the ribosome. RBSDesigner provides a graphical user interface (GUI) for the convenient design of synthetic RBSs.<\/jats:p>\n               <jats:p>Availability: RBSDesigner is written in Python and Microsoft Visual Basic 6.0 and is publicly available as precompiled stand-alone software on the web (http:\/\/rbs.kaist.ac.kr).<\/jats:p>\n               <jats:p>Contact: \u00a0dhlee@kaist.ac.kr<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq458","type":"journal-article","created":{"date-parts":[[2010,8,12]],"date-time":"2010-08-12T00:32:12Z","timestamp":1281573132000},"page":"2633-2634","source":"Crossref","is-referenced-by-count":149,"title":["<i>RBSDesigner<\/i>: software for designing synthetic ribosome binding sites that yields a desired level of protein expression"],"prefix":"10.1093","volume":"26","author":[{"given":"Dokyun","family":"Na","sequence":"first","affiliation":[{"name":"Department of Bio and Brain Engineering, KAIST, 373-1 335-Gwahangno, Yuseong-gu, Daejeon 305-701, South Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Doheon","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Bio and Brain Engineering, KAIST, 373-1 335-Gwahangno, Yuseong-gu, Daejeon 305-701, South Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2010,8,11]]},"reference":[{"key":"2023012507564032100_B1","doi-asserted-by":"crossref","first-page":"7668","DOI":"10.1073\/pnas.87.19.7668","article-title":"Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis","volume":"87","author":"De Smit","year":"1990","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012507564032100_B2","first-page":"512","article-title":"Strategies for achieving high-level expression of genes in Escherichia coli","volume":"60","author":"Makrides","year":"1996","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"2023012507564032100_B3","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-60327-429-6_1","article-title":"UNAFold: software for nucleic acid folding and hybridization","volume":"453","author":"Markham","year":"2008","journal-title":"Methods Mol. Biol."},{"key":"2023012507564032100_B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.mib.2010.02.004","article-title":"Construction and optimization of synthetic pathways in metabolic engineering","volume":"13","author":"Na","year":"2010","journal-title":"Curr. Opin. Microbiol."},{"key":"2023012507564032100_B5","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1186\/1752-0509-4-71","article-title":"Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with a desired expression level in prokaryotes","volume":"4","author":"Na","year":"2010","journal-title":"BMC Syst. Biol."},{"key":"2023012507564032100_B6","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1111\/j.1365-2958.1992.tb01561.x","article-title":"Translation initiation in Escherichia coli: sequences within the ribosome-binding site","volume":"6","author":"Ringquist","year":"2006","journal-title":"Mol. Microbiol."},{"key":"2023012507564032100_B7","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1038\/nbt.1568","article-title":"Automated design of synthetic ribosome binding sites to control protein expression","volume":"27","author":"Salis","year":"2009","journal-title":"Nat. Biotechnol."},{"key":"2023012507564032100_B8","doi-asserted-by":"crossref","first-page":"e52","DOI":"10.1093\/nar\/gnh050","article-title":"Artificial genetic selection for an efficient translation initiation site for expression of human RACK1 gene in Escherichia coli","volume":"32","author":"Zhelyabovskaya","year":"2004","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/20\/2633\/48853347\/bioinformatics_26_20_2633.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/20\/2633\/48853347\/bioinformatics_26_20_2633.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:57:15Z","timestamp":1674633435000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/20\/2633\/193535"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,8,11]]},"references-count":8,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2010,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq458","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,10,15]]},"published":{"date-parts":[[2010,8,11]]}}}