title: GRiP: a computational tool to simulate transcription factor binding in prokaryotes.
abstract: BACKGROUND
  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).
  
  
  BACKGROUND
  http://logic.sysbiol.cam.ac.uk/grip, program and source code
authors.affiliation: Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, UK. n.r.zabet@gen.cam.ac.uk
authors.forename: Nicolae Radu
authors.initials: NR
authors.lastname: Zabet
authors.forename: Boris
authors.initials: B
authors.lastname: Adryan
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D048168:Escherichia coli K12 / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation; D011387:Prokaryotic Cells / Q000378:metabolism; D011485:Protein Binding; D012984:Software; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D014157:Transcription Factors; D004247:DNA