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of the hinge was otherwise unclear, torsion angles were often examined to help adjust the
selection.
Criterion (2) is a definition of a hinge. Sometimes the hinge was slightly longer than
others, and in those cases we added more residues to the hinge, up to a limit of about five
residues in total. If the hinge was distributed over too many residues such that no one
short stretch could be said to constitute the entire hinge, then the morph was discarded
from the Hinge Atlas, since the motion was not hingelike. Criterion (3) is a practical
requirement of a working hinge. If substantial flexure at points outside the hinge is
required to avoid domain interpenetration, then the choice of hinge location is incorrect,
or the motion is not hinge but rather shear or unclassifiable.
The next question was, how to select the morphs which would be annotated and included
in the Hinge Atlas. The entire Database of Macromolecular Motions (MolMovDB) with
(at the time) over 17000 morphs, could clearly not all be annotated given limited
manpower. Further, only a minority of morphs (albeit a large one) exhibited hinge
bending motion, and even within this group much redundancy existed.
To address these issues and make the annotation work manageable, we first selected a
nonredundant subset of the morphs in MolMovDB by aligning all sequences to NRDB90.
This reduced the dataset to 1000 morphs. This was more manageable, but still the set
contained many proteins which did not exhibit hinge bending motions. Fortunately we
found that the score output by FlexProt, normalized by dividing by the number of
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