ReviewMolecular bioSystems2012
Computational models for large-scale simulations of facilitated diffusion.
Review in Molecular bioSystems, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed.
- Facilitated Diffusion Mechanisms in DNA Base Excision Repair and Transcriptional Activation.Chemical reviews · 2018Review
- Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network.PloS one · 2017Article
- What matters for lac repressor search in vivo--sliding, hopping, intersegment transfer, crowding on DNA or recognition?Nucleic acids research · 2015Article
- Estimating binding properties of transcription factors from genome-wide binding profiles.Nucleic acids research · 2015Article
- Search by proteins for their DNA target site: 1. The effect of DNA conformation on protein sliding.Nucleic acids research · 2014Article
- Facilitated diffusion buffers noise in gene expression.Physical review. E, Statistical, nonlinear, and soft matter physics · 2014Article
- Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression.Computational and structural biotechnology journal · 2014Review
- Physical constraints determine the logic of bacterial promoter architectures.Nucleic acids research · 2014Article
- Article
- The effects of transcription factor competition on gene regulation.Frontiers in genetics · 2013Article
- The influence of transcription factor competition on the relationship between occupancy and affinity.PloS one · 2013Article
- System size reduction in stochastic simulations of the facilitated diffusion mechanism.BMC systems biology · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
The binding of site-specific transcription factors to their genomic target sites is a key step in gene regulation. While the genome is huge, transcription factors belong to the least abundant protein classes in the cell. It is therefore fascinating how short the time frame is that they require to home in on their target sites. The underlying search mechanism is called facilitated diffusion and assumes a combination of three-dimensional diffusion in the space around the DNA combined with one-dimensional random walk on it. In this review, we present the current understanding of the facilitated diffusion mechanism and identify questions that lack a clear or detailed answer. One way to investigate these questions is through stochastic simulation and, in this manuscript, we support the idea that such simulations are able to address them. Finally, we review which biological parameters need to be included in such computational models in order to obtain a detailed representation of the actual process.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.