Analysis of Protein Structures
Using Residue Interaction Networks
Dmitrii Shcherbinin and Alexander Veselovsky
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 Á RIN Á Protein–protein interactions
Allosteric regulation Á Scoring function Á 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
D. Shcherbinin Á A. Veselovsky (&)
Laboratory of Structural Bioinformatics, Institute of Biomedical Chemistry,
Pogodinskaya Str., 10, Moscow, Russia
e-mail: veselov@ibmh.msk.su
© Springer Nature Switzerland AG 2019
C. G. Mohan (ed.), Structural Bioinformatics: Applications in Preclinical Drug
Discovery Process, Challenges and Advances in Computational Chemistry
and Physics 27, https://doi.org/10.1007/978-3-030-05282-9_3
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