pyProGA—A PyMOL plugin for protein residue network analysis
Fig 2
The PRN of the supersystem consisting of monomers A and B and the protein-protein interface (PPI): G = GA ∪ GB ∪ GPPI. GA and GB contain all nodes and edges within protein A and B, respectively. a) GPPI contains vertices from both monomers, but only those vertices, which have at least one edge connecting it to a vertex from the other monomer. The edges in GPPI are only those which connect the subgraphs GA and GB (dashed lines) and no edges within the subgraphs GA, GB. Hence, GPPI is a bipartite graph. Part b) shows how blocks in the adjacency matrix A correspond to parts of G and the adjacency matrix APPI of GPPI (circles indicating edges in GPPI).