Protein-nucleic acid complexes: Docking and binding affinity

Protein-nucleic interactions play essential roles in several biological processes, such as gene regulation, replication, transcription, repair and packaging. The knowledge of three-dimensional structures of protein-nucleic acid complexes and their binding affinities helps to understand these functions. In this review, we focus on two major aspects namely, (i) deciphering the three-dimensional structures of protein-nucleic acid complexes and (ii) predicting their binding affinities. The first part is devoted to the state-of-the-art methods for predicting the native structures and their performances including recent CASP targets. The second part is focused on different aspects of investigating the binding affinity of protein-nucleic acid complexes: (i) databases for thermodynamic parameters to understand the binding affinity, (ii) important features determining protein-nucleic acid binding affinity, (iii) predicting the binding affinity of protein-nucleic acid complexes using sequence and structure-based parameters and (iv) change in binding affinity upon mutation. It includes the latest developments in protein-nucleic acid docking algorithms and binding affinity predictions along with a list of computational resources for understanding protein-DNA and protein-RNA interactions.