Computational approaches for understanding the recognition mechanism of protein-nucleic acid complexes

Protein-nucleic acid (NA) interactions are involved in several cellular processes including gene regulation, replication, packaging and control. The functions of protein-NA complexes are studied with the interactions between proteins and NAs using experimental methods and computational techniques. In this chapter, we survey the databases reported in the literature based on structures, binding and affinity. In addition, the contribution of noncovalent interactions to the binding of protein-NA complexes and disorder-to-order transitions (DOTs) upon the complex formation has been reviewed. Further, we discuss various mechanisms proposed to understand the recognition of protein-NA complexes and the importance of molecular dynamics (MD) simulations to gain deep insights. The role of different features to relate the binding affinity of protein-DNA complexes has also been explored. In essence, this comprehensive review provides ample insights to understand the structure-function relationship in protein-NA complexes.