Zabet, Nicolae Radu and Adryan, Boris (2012) GRiP: a computational tool to simulate transcription factor binding in prokaryotes. Bioinformatics, 28 (9). pp. 1287-1289. DOI https://doi.org/10.1093/bioinformatics/bts132
Zabet, Nicolae Radu and Adryan, Boris (2012) GRiP: a computational tool to simulate transcription factor binding in prokaryotes. Bioinformatics, 28 (9). pp. 1287-1289. DOI https://doi.org/10.1093/bioinformatics/bts132
Zabet, Nicolae Radu and Adryan, Boris (2012) GRiP: a computational tool to simulate transcription factor binding in prokaryotes. Bioinformatics, 28 (9). pp. 1287-1289. DOI https://doi.org/10.1093/bioinformatics/bts132
Abstract
<jats:title>Abstract</jats:title> <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> <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> <jats:p>Availability: http://logic.sysbiol.cam.ac.uk/grip, program and source code</jats:p> <jats:p>Contact: n.r.zabet@gen.cam.ac.uk</jats:p> <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p>
Item Type: | Article |
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Uncontrolled Keywords: | Prokaryotic Cells; Escherichia coli K12; Transcription Factors; DNA; Gene Expression Regulation; Binding Sites; Base Sequence; Protein Binding; Algorithms; Computer Simulation; Software |
Subjects: | Q Science > QA Mathematics > QA76 Computer software Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics |
Divisions: | Faculty of Science and Health Faculty of Science and Health > Life Sciences, School of |
SWORD Depositor: | Unnamed user with email elements@essex.ac.uk |
Depositing User: | Unnamed user with email elements@essex.ac.uk |
Date Deposited: | 01 Oct 2015 14:04 |
Last Modified: | 07 Aug 2024 20:37 |
URI: | http://repository.essex.ac.uk/id/eprint/15110 |
Available files
Filename: Bioinformatics-2012-Zabet-bioinformatics_bts132.pdf
Licence: Creative Commons: Attribution-Noncommercial 3.0
Filename: grip_bioinformatics_supp.pdf