Computational analysis of protein hotspots.

Mapping protein hotspots and analysis of the binding free energy associated with each hotspot can provide critical information for drug design. In the present study, we have performed computational analysis for the two known hotspots in thermolysin. Our data showed that the free energy double-decoupling method can determine the binding free energy of different probe molecules associated with the same hotspot or different hotspots with the same probe molecule. The less expensive cosolvent mapping method can be used to readily identify known protein hotspots without prior knowledge and also provide a good estimate of the binding free energy, as compared to the more expensive free energy double-decoupling method. Hence, the combination of the cosolvent mapping method to identify potential protein hotspots followed by more rigorous calculation of the binding free energy associated with each hotspot using the double-decoupling method can provide very useful information for drug design.