{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T14:39:19Z","timestamp":1774967959367,"version":"3.50.1"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2018,4,10]],"date-time":"2018-04-10T00:00:00Z","timestamp":1523318400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100004853","name":"Chinese University of Hong Kong","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004853","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Toehold switches are a class of RNAs with a hairpin loop that can be unfolded upon binding a trigger RNA, thereby exposing a ribosome binding site (RBS) and permitting translation of the reporter protein. They have been shown very useful in detecting a variety of targets including RNAs from Zika and Ebola viruses. The base complementation between the toehold switch and the trigger RNA also makes it sensitive to sequence variations. Design of toehold switches involves a series of considerations related to their sequence properties, structures and specificities.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here we present the first comprehensive web tool for designing toehold switches. We also propose a score for predicting the efficacy of designed toehold switches based on properties learned from \u223c180 experimentally tested switches.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The toehold switch web tool is available at https:\/\/yiplab.cse.cuhk.edu.hk\/toehold\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty216","type":"journal-article","created":{"date-parts":[[2018,4,4]],"date-time":"2018-04-04T11:09:49Z","timestamp":1522840189000},"page":"2862-2864","source":"Crossref","is-referenced-by-count":40,"title":["A comprehensive web tool for toehold switch design"],"prefix":"10.1093","volume":"34","author":[{"given":"Andrew Ching-Yuet","family":"To","sequence":"first","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong"}]},{"given":"David Ho-Ting","family":"Chu","sequence":"additional","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong"}]},{"given":"Angela Ruoning","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong"}]},{"given":"Frances Cheuk-Yau","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong"}]},{"given":"Alan Wai-On","family":"Chiu","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong"}]},{"given":"Daisy Yuwei","family":"Gao","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong"},{"name":"Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong"}]},{"given":"Chung Hang Jonathan","family":"Choi","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong"}]},{"given":"Siu-Kai","family":"Kong","sequence":"additional","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0489-3884","authenticated-orcid":false,"given":"Ting-Fung","family":"Chan","sequence":"additional","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong"}]},{"given":"King-Ming","family":"Chan","sequence":"additional","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5516-9944","authenticated-orcid":false,"given":"Kevin Y","family":"Yip","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong"},{"name":"Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong"}]}],"member":"286","published-online":{"date-parts":[[2018,4,10]]},"reference":[{"key":"2023012712595158100_bty216-B1","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/nature23271","article-title":"Complex cellular logic computation using ribocomputing devices","volume":"548","author":"Green","year":"2017","journal-title":"Nature"},{"key":"2023012712595158100_bty216-B2","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1016\/j.cell.2014.10.002","article-title":"Toehold switches: de-novo-designed regulators of gene 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components","volume":"165","author":"Pardee","year":"2016","journal-title":"Cell"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/16\/2862\/48918235\/bioinformatics_34_16_2862.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/16\/2862\/48918235\/bioinformatics_34_16_2862.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:48:21Z","timestamp":1674827301000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/16\/2862\/4965897"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,4,10]]},"references-count":4,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2018,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty216","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,8,15]]},"published":{"date-parts":[[2018,4,10]]}}}