title: Computational approaches for predicting the binding sites and understanding the recognition mechanism of protein-DNA complexes.
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.
authors.affiliation: Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India. gromiha@iitm.ac.in
authors.forename: M Michael
authors.initials: MM
authors.lastname: Gromiha
authors.forename: R
authors.initials: R
authors.lastname: Nagarajan
mesh_terms: D001665:Binding Sites; D019295:Computational Biology; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D011506:Proteins; D004247:DNA