  We introduce a simple theoretical approach for an equilibrium study of
proteins with known native state structures. We test our approach with results
on well-studied globular proteins, Chymotrypsin Inhibitor (2ci2), Barnase and
the alpha spectrin SH3 domain and present evidence for a hierarchical onset of
order on lowering the temperature with significant organization at the local
level even at high temperatures. A further application to the folding process
of HIV-1 protease shows that the model can be reliably used to identify key
folding sites that are responsible for the development of drug resistance .
