l - People

!
!
!
!
2"
3kBT #Ri $ #R j = (%&1 N&1
) ij = 'k Where
(
k=1
&1
uk [ ] i u k
[ ] j = U) &1 U T
" is the Kirchoff, or connectivity matrix, and " is the diagonal matrix of
eigenvalues " k of ". The elements of " are simple to obtain approximately using the
GNM method.
k.
!
!
!
[ ] !
i is the displacement of the α-carbon of residue i due to normal mode
u k
!
"R i is the net displacement of the α-carbon of residue i from its equilibrium position
due to normal mode motions.
!
168
[1]
" is the effective stiffness used by Tirion et al. Cross-
correlations are normalized with respect to the auto-correlations as follows:
C(i, j) =
"R i # "R j
"R i # "R i "R j # "R j
hNMb requires that we first compute the matrix of average correlations for all continuous
stretches of residues in the protein chain as follows:
[2]