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Hinge Atlas Gold. We have chosen to report all segment boundaries found for N=2,3,4,5.
This means that the hinges resulting from assuming 2,3,4, and 5 domains exist are all
reported on an equal footing. We will delve into the consequences of this in the
discussion.
FlexOracle (FO1, FO1M, FO)
The last of the existing algorithms to be discussed, FlexOracle, is based on the idea that if
structural domains move easily relative to each other, then those domains should be
independently stable. This means that cleaving the protein at the hinge site between
domains should result in fragments that maintain their overall sructure, because those
fragments should have a lower free energy of folding than fragments generated by
cleaving within domains. The algorithm works by estimating the free energy of folding
for all possible pairs of fragments generated by cutting at two points on the protein chain,
and looking for minima of this quantity.
FlexOracle has powerful discriminating ability. Separate work describes three variants of
FlexOracle. These include the single-cut FlexOracle predictor with the FoldX force field,
which here we call FO1, a second predictor which detects the local minima of the same,
which we call FO1M, and the two-cut FlexOracle predictor, which here we simply call
FO. FO is by far the most accurate of these as we will show.
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