Proteins can be conveniently represented as networks of interacting residues, thus allowing the study of several
network parameters that can shed light onto several of their structural and functional aspects. With respect to the binding
of ligands, which are central for the function of many proteins, network analysis may constitute a possible route to assist
the identification of binding sites. As the bulk of this review illustrates, this has generally been easier for enzymes than for
non-enzyme proteins, perhaps due to the different topological nature of the binding sites of the former over those of the
latter. The article also illustrates how network representations of binding sites can be used to search PDB structures in order
to identify proteins that bind similar molecules and, lastly, how codifying proteins as networks can assist the analysis
of the conformational changes consequent to ligand binding.
Keywords: Binding, centrality, cliques, networks, enzymes, ligands, proteins, receptors.
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