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predictor results. Some of these discrepancies are discussed in the Discussion of specific
proteins section. First, however, we evaluate the performance of FlexOracle on the HAG
as a whole.
Statistical evaluation
As mentioned in the Methods section, FlexOracle assumes hinges do not simply
correspond to points of globally lowest energy, but rather to local minima identified and
postprocessed in various ways. The set of residues reported as predicted hinge locations
by any of the three versions of FlexOracle are referred to as test positives, and the number
of residues in this set we will call M. the residues annotated as hinges in the HAG are
referred to as gold standard positives, and the number of these we will call H. In this
section we compare the test positives to the gold standard positives to objectively
evaluate the predictor. Before we do do so, however, we need to define a few more
standard statistical terms as they relate to the current context:
Gold standard negatives: The residues in HAG that are NOT annotated as hinges.
TP (true positives): The number of residues that were both test positives and gold
standard positives.
FP (false positives): The number of residues which were test positives and gold standard
negatives.
TN (true negatives): Number of residues which were test negatives and gold standard
negatives.
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