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With regard to the p-value, the reader should recall that this quantity changes based on
the size of the dataset. Therefore this number can only be used to compare predictors
tested on the same data. By this measure, FO was by far the most discriminating
predictor, followed by hNMb.
As explained earlier, the sensitivity, specificity, and p-value were computed under the
strict criterion for statistical rigor. However, for an application most users would
probably consider a prediction that came within about 5 residues of the correct hinge
location to be a true positive. So we examined each of the 40 proteins and labelled each
as a success, partial success, or failure on the basis of a loose criterion for each predictor
c. A test was considered a success under this criterion if each prediction came within 5
residues of an annotated HAG hinge, and vice versa. It was a partial success if at least
one prediction matched one HAG hinge, but one or more predictions were more than five
residues from a HAG hinge, or vice versa. It was a failure if no predictions were within
five residues of a HAG hinge. The evaluation for each protein under the loose criterion is
presented in supplementary Table 4.5.
We counted the number of successes, partial successes, and failures for the five most
interesting predictors in Table 4.4. As can be seen, FO scored the most successes,
followed by hNMd and hNMb. TLSMD had no successes, but this is due to the fact that
as implemented on our server it reports all domain boundaries for up to 5 domains. Since
the proteins in HAG have at most 3 hinges, some of the TLSMD predictions would be
expected to have no corresponding HAG hinge.
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