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However, this restriction was ignored for purposes of generating HingeMaster
predictions.
Before the above analysis is carried out, StoneHinge performs some preprocessing steps
as follows. It first removes all heteroatoms from the Protein Data Bank formatted
structure files. These include inhibitors, ligands, and cofactors, as they may stabilize the
protein in the ligand-bound conformation and cause the hinge region to no longer appear
flexible. Additionally, it adds hydrogen atoms to the structure using GROMACS, as they
are required to calculate hydrogen bond energies, which are dependent on angular
geometry as well as distance. Lastly, it removes all water molecules from input crystal
structures. While ProFlex works best with only internal water molecules included, which
can potentially be important for stabilizing protein structure, the effects of these waters
are typically minimal. As little difference was found in the hinge predictions when using
vs. omitting entrained water molecules, these were not included for this analysis. Further
explanation and examination of the StoneHinge algorithm may be found in Keating et al.
TLSMD
The second existing method was recently introduced (TLSMD version 0.8.1 was used
here) to identify segments of a protein that exhibit concerted vibrational motion[41]. It is
based on analysis of the spatial distribution of atomic displacement parameters within a
single, conventionally-refined protein crystal structure. Each group so identified is
modeled by assigning to it a set of 20 TLS (Translation/Libration/Screw) parameters that
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