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GRiP: a computational tool to simulate transcription factor binding in prokaryotes

Zabet, Nicolae Radu and Adryan, Boris (2012) 'GRiP: a computational tool to simulate transcription factor binding in prokaryotes.' Bioinformatics, 28 (9). pp. 1287-1289. ISSN 1367-4803

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Abstract

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). 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). © The Author(s) 2012. Published by Oxford University Press.

Item Type: Article
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: Elements
Depositing User: Elements
Date Deposited: 01 Oct 2015 14:04
Last Modified: 15 Jan 2022 00:34
URI: http://repository.essex.ac.uk/id/eprint/15110

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