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however, since we found that the Continuous Domain Boundary Identifier (hNMb)
described above yielded better results when measured by the associated p-values.
The Hinge Atlas Gold
As we mentioned, in order to benchmark (and later combine) hNM and the other
prediction algorithms we need a set of morphs (pairs of homologous proteins with
interpolated motion trajectories) with annotated hinges to use as a gold standard. The
Hinge Atlas Gold (HAG) set was constructed specifically for testing structure-based
hinge predictors, as is explained in detail in prior work. The name of the HAG suggests
its origin in the Hinge Atlas, a larger but less carefully curated set of annotated morphs
used for sequence-based hinge studies. Many of the HAG proteins were collected from
the Hinge Atlas, while others, such as Adenylate Kinase, Biotin Carboxylase, Lactoferrin,
and Calmodulin, are classic hinge bending proteins widely used as test cases in the
community and were added where absent to make the dataset represent proteins of broad
interest as much as possible. The use of protein motions studied by third parties confirms
that the annotated hinge points reflect biologically or at least thermodynamically relevant
dynamics. We delve into this in greater depth for two proteins in this chapter, and several
more in the supplementary discussion. We will show that in some cases, we predict a
hinge where none is annotated in the HAG, but for which some evidence exists in the
literature. In these cases that HAG annotation was not modified, since the point of the
HAG is to be objective rather than comprehensive. These cases suggest that the
predictors can sometimes detect previously unknown motion.
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