  From the crystal structure data and using the concept of equilbrium
statistical mechanics we show how to calculate the thermodynamics of
protein/DNA complexes. We apply the method to the TATA-box binding protein
(TBP)/TATA sequence complex. We have estimated the change in free energy and
entropy for each of the base pair (bp). The local rigidity of the DNA is
estimated from the curvature of the free energy. We also estimate the free
energy gain of the protein due to bond formation with a particular bp. We thus
figure out the bps responsible for specific binding.
