[20], residue interaction networks [21]. In this review, we will use the residue
interaction networks (RINs) to distinguish it from network of protein–protein
interactions.
The application of RIN method in drug design is just at a beginning. RINs have
been used to analyze protein stability and folding [22, 23], 3D structure modeling
[19, 23], finding functionally important amino acid residues and sites [14, 24],
analyzed protein–protein interactions [25], allosteric regulation [26], influence of
amino acid mutations [27]. These studies showed that RIN method is valuable
approaches allowed to improve the drug discovery process. Recently, several
reviews on RINs have been published [28–31].
Herein, we aim to review the investigation of the construction, analysis, and
application of RINs in fields related to drug design.
2 Graph Theory and Residue Interaction Network
Graph theory represents complex system as a set of elements (called vertices or
nodes) with their connections (called edges). Each node can be connected to each
other through multiple edges. Adding order of nodes in the graph, we get a directed
graph, where edges are directed and usually represented as arrows. Introduction of
the quantitative characteristics of the edges results in a weighted graph. Nodes with
edges form a network. The network representation helps to analyze the interaction
among individual elements and to characterize the whole system.
Fig. 1 Structure of SH2 domain of proto-oncogene tyrosine-protein kinase SRC (PDB ID 1o41)
in cartoon (A) and RIN representation
Analysis of Protein Structures Using Residue Interaction …
57
interaction networks (RINs) to distinguish it from network of protein–protein
interactions.
The application of RIN method in drug design is just at a beginning. RINs have
been used to analyze protein stability and folding [22, 23], 3D structure modeling
[19, 23], finding functionally important amino acid residues and sites [14, 24],
analyzed protein–protein interactions [25], allosteric regulation [26], influence of
amino acid mutations [27]. These studies showed that RIN method is valuable
approaches allowed to improve the drug discovery process. Recently, several
reviews on RINs have been published [28–31].
Herein, we aim to review the investigation of the construction, analysis, and
application of RINs in fields related to drug design.
2 Graph Theory and Residue Interaction Network
Graph theory represents complex system as a set of elements (called vertices or
nodes) with their connections (called edges). Each node can be connected to each
other through multiple edges. Adding order of nodes in the graph, we get a directed
graph, where edges are directed and usually represented as arrows. Introduction of
the quantitative characteristics of the edges results in a weighted graph. Nodes with
edges form a network. The network representation helps to analyze the interaction
among individual elements and to characterize the whole system.
Fig. 1 Structure of SH2 domain of proto-oncogene tyrosine-protein kinase SRC (PDB ID 1o41)
in cartoon (A) and RIN representation
Analysis of Protein Structures Using Residue Interaction …
57