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The hinge locations themselves were chosen such that rotations of the structural domains
about the hinge points could approximately reproduce the motions observed in the
morph. Thus these are points of flexibility that permit twisting as well as bending.
Integration of HingeMaster
StoneHinge
Having introduced the novel hNM family of predictors, we move on to describe the
existing predictors. The first of these is StoneHinge, which predicts hinges using the
FIRST algorithm as implemented in the freely available ProFlex software. ProFlex is
designed to analyze flexibility in proteins and uses a 3D constraint counting algorithm
arising from rigidity and graph theory. This approach ultimately derives from the
structural engineering work of James Clerk Maxwell[77], designed to assess whether the
trusswork of a bridge would be adequate to ensure stability. The same concepts have
been shown to be mathematically robust for analyzing the 3-dimensional covalent and
non-covalent bond networks in proteins[78]. The FIRST algorithm[79] thus counts local
degrees of bond-rotational freedom. This divides the protein into two types of regions:
those that are constrained and therefore rigid, and those that are underconstrained and
therefore free to rotate. A rigid region consists of a group of atoms that do not move
relative to each other due to the constraints of the bond network. However, two rigid
regions may move relative to each other, like two stones connected by a flexible tether.
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