{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,26]],"date-time":"2023-01-26T05:20:43Z","timestamp":1674710443062},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1661,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Transcription factors (TFs) are proteins that regulate gene activity by binding to specific sites on the DNA. Understanding the way these molecules locate their target site is of great importance in understanding gene regulation. We developed a comprehensive computational model of this process and estimated the model parameters in (N.R.Zabet and B.Adryan, submitted for publication).<\/jats:p>\n               <jats:p>Results: GRiP (gene regulation in prokaryotes) is a highly versatile implementation of this model and simulates the search process in a computationally efficient way. This program aims to provide researchers in the field with a flexible and highly customizable simulation framework. Its features include representation of DNA sequence, TFs and the interaction between TFs and the DNA (facilitated diffusion mechanism), or between various TFs (cooperative behaviour). The software will record both information on the dynamics associated with the search process (locations of molecules) and also steady-state results (affinity landscape, occupancy-bias and collision hotspots).<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/logic.sysbiol.cam.ac.uk\/grip, program and source code<\/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\/bts132","type":"journal-article","created":{"date-parts":[[2012,3,17]],"date-time":"2012-03-17T00:32:05Z","timestamp":1331944325000},"page":"1287-1289","source":"Crossref","is-referenced-by-count":8,"title":["GRiP: a computational tool to simulate transcription factor binding 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":[[2012,3,16]]},"reference":[{"key":"2023012512303970400_B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1109\/ICBBE.2010.5518098","article-title":"An efficient model for investigating specific site binding of transcription factors","volume-title":"2010 4th International Conference on, Bioinformatics and Biomedical Engineering (iCBBE).","author":"Barnes","year":"2010"},{"key":"2023012512303970400_B2","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1016\/0022-2836(87)90354-8","article-title":"Selection of DNA binding sites by regulatory proteins statistical-mechanical theory and application to operators and promoters","volume":"193","author":"Berg","year":"1987","journal-title":"J. Mol. Biol."},{"key":"2023012512303970400_B3","doi-asserted-by":"crossref","first-page":"6929","DOI":"10.1021\/bi00527a028","article-title":"Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. models and theory","volume":"20","author":"Berg","year":"1981","journal-title":"Biochemistry"},{"key":"2023012512303970400_B4","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1016\/j.jtbi.2008.11.026","article-title":"Models of transcription factor binding: sensitivity of activation functions to model assumptions","volume":"257","author":"Chu","year":"2009","journal-title":"J. Theor. Biol."},{"key":"2023012512303970400_B5","doi-asserted-by":"crossref","first-page":"2999","DOI":"10.1039\/b921303a","article-title":"Facilitated search of proteins on DNA: correlations are important","volume":"12","author":"Das","year":"2010","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2023012512303970400_B6","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1126\/science.1141967","article-title":"Probing transcription factor dynamics at the single-molecule level in a living cell","volume":"316","author":"Elf","year":"2007","journal-title":"Science"},{"key":"2023012512303970400_B7","doi-asserted-by":"crossref","first-page":"12015","DOI":"10.1073\/pnas.192693599","article-title":"Physical constraints and functional characteristics of transcription factor-DNA interaction","volume":"99","author":"Gerland","year":"2002","journal-title":"PNAS"},{"key":"2023012512303970400_B8","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1021\/j100540a008","article-title":"Exact stochastic simulation of coupled chemical reactions","volume":"81","author":"Gillespie","year":"1977","journal-title":"J. Phys. Chem."},{"key":"2023012512303970400_B9","doi-asserted-by":"crossref","first-page":"434013","DOI":"10.1088\/1751-8113\/42\/43\/434013","article-title":"How a protein searches for its site on DNA: the mechanism of facilitated diffusion","volume":"42","author":"Mirny","year":"2009","journal-title":"J. Phys. A, Math. Theor."},{"key":"2023012512303970400_B10","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1093\/bioinformatics\/16.1.16","article-title":"DNA binding sites: representation and discovery","volume":"16","author":"Stormo","year":"2000","journal-title":"Bioinformatics"},{"key":"2023012512303970400_B11","doi-asserted-by":"crossref","first-page":"4350","DOI":"10.1529\/biophysj.106.086157","article-title":"Diffusion of transcription factors can drastically enhance the noise in gene expression","volume":"91","author":"van Zon","year":"2006","journal-title":"Biophys. J."},{"key":"2023012512303970400_B12","doi-asserted-by":"crossref","first-page":"3570","DOI":"10.1093\/nar\/gkn173","article-title":"Spatial effects on the speed and reliability of protein-DNA search","volume":"36","author":"Wunderlich","year":"2008","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/9\/1287\/48874754\/bioinformatics_28_9_1287.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/9\/1287\/48874754\/bioinformatics_28_9_1287.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T15:57:55Z","timestamp":1674662275000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/9\/1287\/313146"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,3,16]]},"references-count":12,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2012,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts132","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,5,1]]},"published":{"date-parts":[[2012,3,16]]}}}