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eigenvector. The resulting reordering of rows and columns of the contact matrix is such
that residues tend to be grouped with those they are in contact with, regardless of their
place in the protein sequence. The matrix then consists of only two submatrices, and the
numerical problem is only that of finding the optimal boundary between them. The
optimal choice of boundary is that which maximizes the period of oscillation of an
equivalent two-mass-spring system per supplementary Equation 9:
" = µ
#10
I12 $12 s [9]
Where the reduced mass is used:
µ = N1N2 . [10]
N1 + N2 Here
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N 1 and
N 2 are the number of residues in the first and second submatrices, and
the sum of the interface contacts.
After reordering there is only a single boundary, and thus only N evaluations of τ are
needed, whereas without this reordering some power of N evaluations would be needed.
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