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coordinate neighbors in a very stable and position-specific manner. We therefore
recommend care be taken when using this method for predicting hinges in metal-bound
structures, when those metals appear to heavily affect the structural and motional
characteristics of the protein.
Web interface
Users may submit PDB-formatted files through our Hinge Prediction page, linked to from
the MolMovDB.org front page. They will receive an email with instructions on how to
view graphs similar to those shown in figures 3-8. In brief, the morph page contains a
‘Hinge Analysis’ tab which in turn has a link to the FlexOracle results. Blue diamonds
on the single-cut predictor graph indicate the minima of the single-cut FoldX free energy
per the criterion used in this work. Hinges tend to coincide with minima of the single-cut
FlexOracle energy graph, as is explained in the Discussion of specific proteins section At
this time only the single-cut predictor is run automatically on all submissions, but users
may contact the author to have the two-cut predictor run on any submitted protein. The
user should bear in mind that results may be of limited accuracy for membrane proteins
and proteins bound to complexes or large substrates. If metals strongly affect the
stability and motion of the protein, as is the case for EF hands, this may also limit
accuracy. Lastly, if the hinge seems sterically unreasonable the reader should consider
the possibility that the hinge has three or more strands or the motion is not hingelike.
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