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Analysis of Protein Structures Using Residue Interaction Networks

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Structural Bioinformatics: Applications in Preclinical Drug Discovery Process

Part of the book series: Challenges and Advances in Computational Chemistry and Physics ((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.

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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. Laboratory of Structural Bioinformatics, Institute of Biomedical Chemistry, Pogodinskaya Str., 10, Moscow, Russia

    Dmitrii Shcherbinin & Alexander Veselovsky

Authors
  1. Dmitrii Shcherbinin
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  2. Alexander Veselovsky
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Correspondence to Alexander Veselovsky .

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Editors and Affiliations

  1. Amrita Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Kochi, India

    C. Gopi Mohan

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Shcherbinin, D., Veselovsky, A. (2019). Analysis of Protein Structures Using Residue Interaction Networks. In: Mohan, C. (eds) Structural Bioinformatics: Applications in Preclinical Drug Discovery Process. Challenges and Advances in Computational Chemistry and Physics, vol 27. Springer, Cham. https://doi.org/10.1007/978-3-030-05282-9_3

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