Which software is commonly used to calculate the protein complex buried area?

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Akshay Bhat

One such software that I know of is called NACCESS (http://www.bioinf.manchester.ac.uk/naccess/). There is a review for it as well. (http://www.ncbi.nlm.nih.gov/pubmed/23389845). Though protein protein interactions, this could very well be a starting point to understand how to use it for Protein-DNA interactions.

Avinash S. Punekar

Try PDBe PISA server (http://www.ebi.ac.uk/msd-srv/prot_int/) for more comprehensive results for macromolecular interfaces.