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potential for simplification, motion prediction for these has remained largely an unsolved
problem. We resolve the motion by first detecting the hinge, then accelerating the rigid
body motions of the domains.
Early evolutionary studies indicated that the stabilizing interactions within domains were
more important than interactions at the hinge. This was consistent with the general
consensus that structural domains are independently stable. Our first method for
detecting the domain boundaries consisted of breaking the protein into two fragments by
making some of the many possible combinations of two cuts on the backbone and then
separating the resulting two fragments (one continuous and one discontinuous[112]) and
computing their stabilities. We found that indeed the cuts that coincided with the hinge
resulted in the most stable fragments.
In a second method, we studied the correlations of atoms assuming a Hookean potential.
Under these circumstances not only the spectral decomposition but also the equipartition
theorem apply. The motional correlations of residues in a thermal ensemble generated in
the eigenvector basis were analyzed with a view to finding a single domain of maximal
size with high average interresidue correlation.
Additional methods were developed, and some existing methods were tested. In Chapter
4 we integrate all of these into a single combined method which emits several hinge
predictions and assigns a confidence score to each.
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