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Methods
Preparation of computer annotated hinge dataset
Prior to generating the manually annotated Hinge Atlas, we used computational methods
to generate a dataset of hinge residues for our statistical studies. We began by running
FlexProt[26], a leading hinge identification tool, on all morphs (pairs of homologous
protein structures) in the Database of Macromolecular Motions. FlexProt works by
matching and structurally aligning fragments in one structure with corresponding
fragments in the other. The goal is to find fragment pairs which (1) have minimal RMSD
and (2) are maximal in size. The hinges are then reported as the boundaries separating
those fragments. Goal (2) is equivalent to minimizing the number of these hinges. Since
domains are never completely rigid, RMSD tends to grow with fragment size and
therefore goal (1) is in conflict with goal (2). This conflict is dealt with by providing the
user with a series of adjustable parameters, and further by reporting not one but several
alternative hinge locations from which the user can choose. We used a combination of
computer and manual culling to select those morphs for which the identified hinges met
the following criteria:
Motion was domain wise, i.e. two or more structural domains could be observed moving
approximately as rigid bodies with respect to each other.
The identified hinge was located in the flexible region connecting two rigid domains,
rather than in the domains themselves.
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