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Open Access Highly Accessed Database

TFinDit: transcription factor-DNA interaction data depository

Daniel Turner, RyangGuk Kim and Jun-tao Guo*

Author affiliations

Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA

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Citation and License

BMC Bioinformatics 2012, 13:220  doi:10.1186/1471-2105-13-220

Published: 3 September 2012

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.

Keywords:
Transcription factor; Database; Binding site prediction; Interaction potential