2.4 Global network and structure comparison
Structures in their bound form are aligned with the corresponding
structures in their unbound form and information of structural deviation
(RMSD) between all pairs of chains are obtained. TM-align is used to
compute the RMSD, which is a measure of Cα deviation between
topologically equivalent residues. This is followed by global network
comparison of the same equivalent residues using the network
dissimilarity method discussed by Gadiyaram and coworkers.
The method of computing network dissimilarity involves storing the PSN
as an adjacency matrix which is normalised to a Laplacian of the network
graph followed by its spectral decomposition to obtain the eigen values
and eigen vectors. A Forbenious norm of the difference between the
adjacency matrices of the two structural networks provides the edge
difference score (EDS). A difference in the local and global clustering
of residues in the network is captured using the Edge-weighted cosine
score (EWCS) and the correspondence scores respectively. The component
scores are then used to compile the Network Dissimilarity Score (NDS)
between the compared networks. Identical networks would have a NDS of
zero. No two networks can have a dissimilarity greater than\(\sqrt{}3\).