Discovery Studio tools can be used to help identify mutations that will either improve or disrupt protein-protein binding. Moreover these calculations may be performed at various pH values. The molecular mechanics method employed in Discovery Studio takes into account the pH-dependency of protein ionization and in turn, protein binding energies.

This method, application and comparison to experimental results is describes in the following paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601434/