Hi,
I've been working in a computational lab for the past year on the work you are interested in. Generally, there are a lot of labs working on protein folding/stability and protein dynamics. One of the most powerful softwares for doing protein energetic assessments is the Rosetta, which was developed by a suite of academic labs. The primary lab is at the University of Washington, but there are many great Rosetta labs in other places, including UNC Chapel Hill, Johns Hopkins University, and University of California San Francisco. The following list is composed of the programs I think are strongest in this area, not in any specific order:
UCAL San Francisco
UNC Chapel Hill
University of Washington
Johns Hopkins University
UCAL San Diego
Stanford University
Hope this helps out.