ArticleNucleic acids research2012
3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 19 citations in OpenAlex.
- Structure-based learning to predict and model protein-DNA interactions and transcription-factor co-operativity inNAR genomics and bioinformatics · 2024Article
- Traversing DNA-Protein Interactions Between Mesophilic and Thermophilic Bacteria: Implications from Their Cold Shock Response.Molecular biotechnology · 2024Article
- EMQIT: a machine learning approach for energy based PWM matrix quality improvement.Biology direct · 2017Article
- An Empirical Prior Improves Accuracy for Bayesian Estimation of Transcription Factor Binding Site Frequencies within Gene Promoters.Bioinformatics and biology insights · 2015Article
- Article
- Structure-based modeling of protein: DNA specificity.Briefings in functional genomics · 2015Review
- Epigenome-guided analysis of the transcriptome of plaque macrophages during atherosclerosis regression reveals activation of the Wnt signaling pathway.PLoS genetics · 2014Article
- PiDNA: Predicting protein-DNA interactions with structural models.Nucleic acids research · 2013Article
- Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites.Plant methods · 2013Article
- Using potential master regulator sites and paralogous expansion to construct tissue-specific transcriptional networks.BMC systems biology · 2012Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present the webserver 3D transcription factor (3DTF) to compute position-specific weight matrices (PWMs) of transcription factors using a knowledge-based statistical potential derived from crystallographic data on protein-DNA complexes. Analysis of available structures that can be used to construct PWMs shows that there are hundreds of 3D structures from which PWMs could be derived, as well as thousands of proteins homologous to these. Therefore, we created 3DTF, which delivers binding matrices given the experimental or modeled protein-DNA complex. The webserver can be used by biologists to derive novel PWMs for transcription factors lacking known binding sites and is freely accessible at http://www.gene-regulation.com/pub/programs/3dtf/.
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