{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T22:24:48Z","timestamp":1761863088268},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1640,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Gene activity is mediated by site-specific transcription factors (TFs). Their binding to defined regions in the genome determines the rate at which their target genes are transcribed.<\/jats:p>\n               <jats:p>Results: We present a comprehensive computational model of the search process of TF for their genomic target site(s). The computational model considers: the DNA sequence, various TF species and the interaction of the individual molecules with the DNA or between themselves. We also demonstrate a systematic approach how to parametrize the system using available experimental data.<\/jats:p>\n               <jats:p>Contact: \u00a0n.r.zabet@gen.cam.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts178","type":"journal-article","created":{"date-parts":[[2012,4,8]],"date-time":"2012-04-08T08:06:13Z","timestamp":1333872373000},"page":"1517-1524","source":"Crossref","is-referenced-by-count":17,"title":["A comprehensive computational model of facilitated diffusion in prokaryotes"],"prefix":"10.1093","volume":"28","author":[{"given":"Nicolae Radu","family":"Zabet","sequence":"first","affiliation":[{"name":"1 Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR and 2Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK"},{"name":"1 Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR and 2Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK"}]},{"given":"Boris","family":"Adryan","sequence":"additional","affiliation":[{"name":"1 Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR and 2Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK"},{"name":"1 Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR and 2Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK"}]}],"member":"286","published-online":{"date-parts":[[2012,4,6]]},"reference":[{"key":"2023012512311983800_B1","doi-asserted-by":"crossref","first-page":"e1000705","DOI":"10.1371\/journal.pcbi.1000705","article-title":"Detailed simulations of cell biology with smoldyn 2.1","volume":"6","author":"Andrews","year":"2010","journal-title":"PLoS Comput. 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