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.