  Interactions between proteins are hard to decipher. Protein-protein
interactions are difficult problem to address because they are not based on
differences in charge type like protein-DNA or protein-lipid interactions. In
this manuscript we present a few methods aimed at recognizing contact and their
neighboring first layer residues. The methods are based on the simplified
analysis of normal modes via the Gaussian Network Model (GNM). The methods
adjust the number of modes used in analysis on the basis of the comparison of
predicted and expected number of targets (contact and first layer residues).
The number of modes used in weighted sum calculation is increased or decreased
if the number of predictions falls out of range for a given protein sequence
length. The methods are able to recognize more than 50% of targets on average.
At the same time they generate slightly more than 40% of false positives. They
are also fairly successful in recognizing near native decoys of the Vakser
decoy sets. The results depicted here show that kinetically active residues are
important in protein-protein interactions. The GNM analysis depicted also shows
that the two interacting chains usually exhibit opposite behavior. While the
binding surface of one of the partners is rigid and stable, the interfacial
area of the other partner is more flexible.
