Gromiha MM, Nagarajan R. Computational approaches for predicting the binding sites and understanding the recognition mechanism of protein-DNA complexes.
ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013;
91:65-99. [PMID:
23790211 DOI:
10.1016/b978-0-12-411637-5.00003-2]
[Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein-DNA recognition plays an important role in the regulation of gene expression. Understanding the influence of specific residues for protein-DNA interactions and the recognition mechanism of protein-DNA complexes is a challenging task in molecular and computational biology. Several computational approaches have been put forward to tackle these problems from different perspectives: (i) development of databases for the interactions between protein and DNA and binding specificity of protein-DNA complexes, (ii) structural analysis of protein-DNA complexes, (iii) discriminating DNA-binding proteins from amino acid sequence, (iv) prediction of DNA-binding sites and protein-DNA binding specificity using sequence and/or structural information, and (v) understanding the recognition mechanism of protein-DNA complexes. In this review, we focus on all these issues and extensively discuss the advancements on the development of comprehensive bioinformatics databases for protein-DNA interactions, efficient tools for identifying the binding sites, and plausible mechanisms for understanding the recognition of protein-DNA complexes. Further, the available online resources for understanding protein-DNA interactions are collectively listed, which will serve as ready-to-use information for the research community.
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