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At least two sets of atomic coordinates are available, and together they represent a
domain motion that is biologically relevant or thermodynamically feasible.
The motion involves two or more rigid domains moving about a flexible hinge.
Each of these pairs of protein structures, also known as morphs, has an annotated hinge
location. This location was chosen prior to running any hinge prediction codes, by visual
inspection of the corresponding morph movie. We have found manual annotation to be
more reliable than the use of automated methods such as FlexProt, DynDom, or
Hingefind, which depend on user-adjustable parameters and sometimes incorrectly assign
the hinge location. The process of inspection and annotation was aided by the “Hinge
Annotation Tool” available on the morph page for each morph in MolMovDB. It
consists of a set of arrow buttons which adjust the position of a window of residues,
which are highlighted as the protein moves. This tool can also take annotations from the
public for various uses. The result of the annotation effort is a set of hinge residues for
structural pairs against which FlexOracle and other hinge predictors can be tested.
One must bear in mind that the hinge annotation is not encyclopedic. It is based on the
comparison of two sets of structural coordinates, but other motions not reflected by this
measure may be thermodynamically feasible. In some cases FlexOracle predicted hinges
not annotated in HAG but for which we later found experimental evidence in the
published literature. Since the point of the HAG is to be objective rather than
comprehensive, in these cases we did not change the annotation or our scoring of the
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