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Abstract
Self-avoiding random walks were performed on protein residue networks. Compared with
protein residue networks with randomized links, the probability of a walk being successful
is lower and the length of successful walks shorter in (non-randomized) protein residue
networks. Fewer successful walks and shorter successful walks point to higher communication
specificity between protein residues, a conceivably favourable attribute for proteins
to have. The use of random walks instead of shortest paths also produced lower node
centrality, lower edge betweeness and lower edge load for (non-randomized) protein
residue networks than in their respective randomized counterparts. The implications
of these properties for protein residue networks are discussed in terms of communication
congestion and network vulnerability. The randomized protein residue networks have
lower network clustering than the (non-randomized) protein residue networks. Hence,
our findings also shed light on a hitherto neglected aspect: the importance of high
network clustering in protein residue networks. High clustering increases navigability
of a network for local search and the combination of a local search process on a highly
clustered small-world network topology such as protein residue networks reduces communication
congestion and network vulnerability.