Topological properties of networks in structural classification of proteins

We investigate the complex networks of interacting amino acids in protein structures. This case presents the status of numerical simulations and analyses relevant to the topological properties of networks in the structural classification of proteins. From our result protein networks are shown to have a small-world feature regardless of their structural class. In particular, proteins are found to have a positive assortative coefficient that when applied to the topological property is described as a tendency for connectivity of high-degree nodes. The modularity of the proteins in our case is a significantly increasing function of N. From the resultant network, we mainly estimate the network’s metrics, such as the averaged shortest path length, the averaged clustering coefficient, the local efficiency, the global efficiency, the assortative coefficient, and the modularity.