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primary inter-domain flexibility. Thus a curated interpretation of the TLSMD analysis of
MurA would list three features: A two domain protein with an inter-domain hinge points
at residues 20/21 and 228/229; a secondary set of hinge points corresponding to a flexible
loop (108-127) in one of the domains; and a flexible C-terminus.
StoneHinge
We discussed the fact that TLSMD overpredicts, since it reports more hinges than are
annotated in HAG. StoneHinge also had a significant rate of false-positive hinge
predictions (Table 4.1), This is typically caused by StoneHinge underpredicting the size
of the rigid domains, such as in the open form of ovotransferrin. In that case, StoneHinge
predicted that the second domain spanned residues 121-171. However, observation of
the motion reveals that this domain spans residues 93-245. This underprediction of the
rigid domain leads StoneHinge to overpredict the span of the hinge. Additionally, a
number of StoneHinge’s over- and mis-predictions are flagged as such by StoneHinge.
As noted above, if either rigid domain is predicted to be less than twenty residues,
StoneHinge reports that the predicted hinges are unlikely to correspond to domain motion
(again, this eventuality is ignored for HingeMaster).
We note that when both TLSMD and StoneHinge predict a hinge, two-thirds of the time
it coincides with a HAG hinge. Likewise, most experimentally defined hinges are
predicted by either StoneHinge or TLSMD, accounting for the substantial weight they
receive in HingeMaster. In the cases where either StoneHinge or TLSMD misses a
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