Topological Analyses of Protein-Ligand Binding: a Network Approach

Title:Topological Analyses of Protein-Ligand Binding: a Network Approach

Volume: 17 Issue: 1

Author(s): Stefano Costanzi

Affiliation:

Keywords: Binding, centrality, cliques, networks, enzymes, ligands, proteins, receptors.

Abstract: 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.

Cite this article as:

Costanzi Stefano, Topological Analyses of Protein-Ligand Binding: a Network Approach, Current Protein & Peptide Science 2016; 17 (1) . https://dx.doi.org/10.2174/1389203716666150923103934