Prediction of nucleic acid binding proteins and their binding sites

The information on interactions between proteins and nucleic acids in protein-nucleic acid complexes provides deep insights for understanding their functions. Experimentally, several techniques including X-ray crystallography, isothermal titration calorimetry and DNA/RNA footprinting are used to identify nucleic acid binding proteins and their binding sites. On the other hand, computational tools have been developed for annotating nucleic acid-binding proteins to compensate the requirements of manpower, resources and time for experiments. In this chapter, the methods for identifying DNA- or RNA-binding proteins and features used in these algorithms have been reviewed. Different methods for identifying the binding sites in protein-nucleic acid complex structures are outlined along with computational methods for predicting the residues at the interface. We have also listed a set of tools available in the literature for predicting DNA/RNA-binding proteins and their binding sites along with annotating those proteins in genomic sequences.