{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T16:18:49Z","timestamp":1775924329318,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Much is now known about the mechanistic details of gene translation. There are also rapid advances in high-throughput technologies to determine quantitative aspects of the system. As a consequence-realistic and system-wide simulation models of translation are now feasible. Such models are also needed as devices to integrate a large volume of highly fragmented data known about translation.<\/jats:p>\n               <jats:p>Software: In this application note, we present a novel, highly efficient software tool to model translation. The tool represents the main aspects of translation. Features include a representation of exhaustible tRNA pools, ribosome\u2013ribosome interactions and differential initiation rates for different mRNA species. The tool is written in Java, and is hence portable and can be parameterized for any organism.<\/jats:p>\n               <jats:p>Availability: The model can be obtained from the authors or directly downloaded from the authors' home-page (http:\/\/goo.gl\/JUWvI).<\/jats:p>\n               <jats:p>Contact: \u00a0d.f.chu@kent.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr650","type":"journal-article","created":{"date-parts":[[2011,11,24]],"date-time":"2011-11-24T01:41:00Z","timestamp":1322098860000},"page":"292-293","source":"Crossref","is-referenced-by-count":20,"title":["A novel and versatile computational tool to model translation"],"prefix":"10.1093","volume":"28","author":[{"given":"Dominique","family":"Chu","sequence":"first","affiliation":[{"name":"1 School of Computing, University of Kent, Kent CT2 7NF, 2 Department of Genetics, University of Cambridge, CB2 1QR and 3School of Biosciences, University of Kent, Kent CT2 7NJ, UK"}]},{"given":"Nicolae","family":"Zabet","sequence":"additional","affiliation":[{"name":"1 School of Computing, University of Kent, Kent CT2 7NF, 2 Department of Genetics, University of Cambridge, CB2 1QR and 3School of Biosciences, University of Kent, Kent CT2 7NJ, UK"}]},{"given":"Tobias","family":"von der Haar","sequence":"additional","affiliation":[{"name":"1 School of Computing, University of Kent, Kent CT2 7NF, 2 Department of Genetics, University of Cambridge, CB2 1QR and 3School of Biosciences, University of Kent, Kent CT2 7NJ, UK"}]}],"member":"286","published-online":{"date-parts":[[2011,11,22]]},"reference":[{"key":"2023012511515751300_B1","doi-asserted-by":"crossref","first-page":"6705","DOI":"10.1093\/nar\/gkr300","article-title":"The role of tRNA and ribosome competition in coupling the expression of different mRNAs in saccharomyces cerevisiae","volume":"39","author":"Chu","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012511515751300_B2","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1016\/j.compbiolchem.2007.07.003","article-title":"Ribosome kinetics and aa-trna competition determine rate and fidelity of peptide synthesis","volume":"31","author":"Fluitt","year":"2007","journal-title":"Comput. 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