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. 2012 Sep 3:13:220.
doi: 10.1186/1471-2105-13-220.

TFinDit: transcription factor-DNA interaction data depository

Daniel Turner  1 , RyangGuk Kim, Jun-tao Guo
Affiliations

TFinDit: transcription factor-DNA interaction data depository

Daniel Turner et al. BMC Bioinformatics. .

Abstract

Background: One of the crucial steps in regulation of gene expression is the binding of transcription factor(s) to specific DNA sequences. Knowledge of the binding affinity and specificity at a structural level between transcription factors and their target sites has important implications in our understanding of the mechanism of gene regulation. Due to their unique functions and binding specificity, there is a need for a transcription factor-specific, structure-based database and corresponding web service to facilitate structural bioinformatics studies of transcription factor-DNA interactions, such as development of knowledge-based interaction potential, transcription factor-DNA docking, binding induced conformational changes, and the thermodynamics of protein-DNA interactions.

Description: TFinDit is a relational database and a web search tool for studying transcription factor-DNA interactions. The database contains annotated transcription factor-DNA complex structures and related data, such as unbound protein structures, thermodynamic data, and binding sequences for the corresponding transcription factors in the complex structures. TFinDit also provides a user-friendly interface and allows users to either query individual entries or generate datasets through culling the database based on one or more search criteria.

Conclusions: TFinDit is a specialized structural database with annotated transcription factor-DNA complex structures and other preprocessed data. We believe that this database/web service can facilitate the development and testing of TF-DNA interaction potentials and TF-DNA docking algorithms, and the study of protein-DNA recognition mechanisms.

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Figures

Figure 1
Figure 1
Procedure for TFinDit construction and update.
Figure 2
Figure 2
A snapshot of the “Advanced Search” page for TFinDit.
Figure 3
Figure 3
Detailed information for TFinDit entry 3HDD. The red box indicates the quick links to other analysis tools. The blue box shows the cutoff values that users can change and get updated data.
See this image and copyright information in PMC

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References

    1. Pan Y, Tsai CJ, Ma B, Nussinov R. Mechanisms of transcription factor selectivity. Trends Genet. 2010;26:75–83. doi: 10.1016/j.tig.2009.12.003. - DOI - PMC - PubMed
    1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res. 2000;28:235–242. doi: 10.1093/nar/28.1.235. - DOI - PMC - PubMed
    1. Kuntz ID. Structure-based strategies for drug design and discovery. Science. 1992;257:1078–1082. doi: 10.1126/science.257.5073.1078. - DOI - PubMed
    1. Darnell JE Jr. Transcription factors as targets for cancer therapy. Nat Rev Cancer. 2002;2:740–749. doi: 10.1038/nrc906. - DOI - PubMed
    1. Sankpal UT, Goodison S, Abdelrahim M, Basha R. Targeting Sp1 transcription factors in prostate cancer therapy. Med Chem. 2011;7:518–525. doi: 10.2174/157340611796799203. - DOI - PubMed

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