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Analysis of Protein Structures Using Residue Interaction Networks

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

Abstract

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.

Keywords

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

Abbreviations

CAPRI

Critical assessment of predicted interactions

DDN

Differential network

GPCR

G protein-coupled receptor

HPNCscore

Hydrophobic and polar networks combined scoring function

MD

Molecular dynamics simulation

NACEN

Node-weighted amino acid contact energy network

PPI

Protein–protein interaction

RIN

Residue interaction network

SVM

Support vector machine

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Authors and Affiliations

  1. 1.Laboratory of Structural BioinformaticsInstitute of Biomedical ChemistryMoscowRussia

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