Analysis of Protein Structures Using Residue Interaction Networks

  • Dmitrii Shcherbinin
  • Alexander Veselovsky
Part of the Challenges and Advances in Computational Chemistry and Physics book series (COCH, volume 27)


The network description is widely used to analyze the topology and the dynamics of complex systems. Residue interaction network (RIN) represents three-dimensional structure of protein as a set of nodes (residues) with their connections (edges). Calculated topological parameters from RIN correlate with various aspects of protein structure and function. Here, we reviewed the applications of RIN for the analysis and prediction of functionally important residues and ligand binding sites, protein–protein interactions, allosteric regulation, influence of point mutations on structure and dynamics of proteins.


Residue interaction network RIN Protein–protein interactions Allosteric regulation Scoring function Allosteric pathway 



Critical assessment of predicted interactions


Differential network


G protein-coupled receptor


Hydrophobic and polar networks combined scoring function


Molecular dynamics simulation


Node-weighted amino acid contact energy network


Protein–protein interaction


Residue interaction network


Support vector machine


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Authors and Affiliations

  1. 1.Laboratory of Structural BioinformaticsInstitute of Biomedical ChemistryMoscowRussia

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