l - People

!
hNMc goes through the same procedure, except it ignores the lowest minimum (already
reported by hNMb) and processes all remaining minima as above. If any hinge point is
within five residues of a hinge point corresponding to a lower minimum, the hinge point
corresponding to the higher minimum is discarded.
hNMd (Excluded Region Identifier) works somewhat differently. It is based on the idea
that we may not be able to precisely identify the flexible regions of protein, but we can
perhaps still identify parts of the protein which are rigid, and surmise that the hinge may
lie anywhere except in these rigid regions. For a minimum of
it considers residues
k +1 to
170
!
W located at residues
l " 2 to be part of a structural domain and excludes them
from consideration as a hinge. The process is repeated with the remaining minima
W (k,l). Any ! residues ! that were not excluded after all minima have been considered in
this way are reported as potential hinges.
Lastly, hNMe (Holm and Sander-like hinge predictor) partitions the matrix differently
from NMB with similar goals. The correlation matrix (Equation 2) is partitioned by
separating the residues into two domains much as Holm and Sander did for the contact
!
!
k,l,
k,l of
matrix. A minor adjustment is needed which is explained in the Supplementary Methods
section. This results in a reasonably good predictor which has the added benefit of
assigning each residue to one of two domains, and also has no intrinsic limitation with
respect to number of hinge points. We do not describe this method in great detail,