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and hNMb both completely failed to predict the triple stranded hinge in cAMP dependent
protein kinase, while Stonehinge and TLSMD either failed or had partial success. For the
closed form of this protein hNMd was the only successful predictor. For the open form,
one of the three hinge points is in a disordered region that does not appear in the crystal
structure. hNMd has a cluster of hinge predictions centered about that break in the chain
and therefore it was arguably as successful as could be expected under the circumstances.
The same argument could not be made for the other predictors, as the reader can verify
by examining Figure 4.3.
In general, we find that residues identified by hNMd coincide to a high degree with the
general location of the hinge. However the predicted hinge regions were broad, lowering
the specificity and raising the p-value.
TLSMD
As mentioned earlier, because hinges for N=1,2,3,4,5 are reported together, the set of
TLSMD "hinge predictions" for each protein will be larger than the actual number of
hinge points. That is, the forced partition of a 3-domain protein into only 2 segments will
tend to create a “false” breakpoint somewhere inside the middle domain, rather than
finding either of the two “true” domain boundaries. Even if the two correct boundaries
are found by the TLSMD partitions for N≥3, this initial false prediction will remain in the
prediction set. This results in a poorer showing on a ROC curve if the extra predictions
are treated as false positives. An alternative would have been to manually filter out these
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