Table 1. Summary of protein structure networks.

Group and reference(s)	Network	Analysis
Grindley et al. [27]	Protein structure graphs based on secondary-structural elements	Subgraph isomorphism for structure comparison
Dokholyan et al. [33]	Protein structure graphs based on Cα atoms	Network properties and hubs relating to protein folding using graphs of transition states and intermediates
Vendruscolo et al. [31,32]	Protein structure graphs based on Cα atoms	Network properties and hubs relating to protein folding using graphs of transition states and intermediates
Atilgan et al. [29]	Protein structure graphs based on Cα atoms	Shortest path length and clustering coefficients, network properties
Greene and Higman [30]	Protein structure graphs based on atomic details	Network properties, scale-free nature of protein structure graphs
Brinda and Vishveshwara (unpublished work)	Residue-based protein structure graphs	Network properties, scale-free nature, role of hubs in protein structures
Vishveshwara and co-workers [40–45]	Residue-based protein structure graphs	Graph-spectral parameters for detection of amino acid clusters at protein core, protein/protein and protein/DNA interfaces
Sistla et al. [38]	Residue-based protein structure graphs	Identification of structural domains in proteins structures from graph spectra
Reichman et al. [39]	Residue-based protein structure graphs	Modular clusters at protein/protein interfaces
Przytycka et al. [28]	Protein structure graphs based on secondary-structural elements	Rules of protein folding in β-proteins by basic graph manipulations
Bahar et al. [34,35]	Protein structure graphs based on Cα atoms	Graph-spectral parameters for elucidating protein dynamics using the Gaussian network model (GNM) and the anisotropic network model (ANM)
Samudrala and Moult [36,37]	Protein graphs based on steriacally allowed conformations of protein side chains (rotamers)	Clique-detecting algorithm used for modelling the side chains in proteins with unknown structures