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Protein–DNA interactions play important roles in many vital processes, such as the regulation of gene expression, DNA replication and repair, transcription, and packaging. Understanding the specificity with which proteins recognize target DNA sequences is of considerable theoretical and practical importance and its basis has been demonstrated through experimental and computational Analysis theof protein–DNA complexes. Proteins can interact with DNA through electrostatic interactions (salt bridges), dipolar interactions (hydrogen bonding, H-bonds), entropic effects (hydrophobic interactions) and dispersion forces (base stacking).