Network analysis of protein structures identifies functional residues.

By Gil Amitai, A. Shemesh, Einat Sitbon, M. Shklar, D. Netanely, Ilya Venger, Shmuel Pietrokovski. Journal of Molecular Biology, 2004

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Predicting protein function from sequence and structural data. (2005, background): “[35] aims to identify active site residues through network analysis of protein structures.”
Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations (2015, background): “Thus, including structural considerations, possibly ‘local closeness’ as an integrated parameter [71], may greatly improve prediction of the effect of mutations [88, 89], as already shown for certain predictors [8, 89–93].”
Residue centrality, functionally important residues, and active site shape: Analysis of enzyme and non‐enzyme families (2006, methodology): “In addition, this model permits the investigation of the role of each individual amino acid within the complex interacting network Protein (Murzin (Vendruscolo et al. 2002; del Sol and O’Meara 2004).”
Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure (2009, background): “, Theoretical Microscopic Titration Curves (THEMATICS) [35], binding site similarity [36], phage display libraries [37], and residue interaction graphs [38]).”