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Computational and Mathematical Methods in Medicine
Volume 2013, Article ID 365410, 9 pages
Research Article

The Effect of Edge Definition of Complex Networks on Protein Structure Identification

1College of Chemistry, Sichuan University, Chengdu 610064, China
2College of Computer Science, Sichuan University, Chengdu 610064, China

Received 6 December 2012; Revised 23 January 2013; Accepted 25 January 2013

Academic Editor: Guang Hu

Copyright © 2013 Jing Sun et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


The main objective of this study is to explore the contribution of complex network together with its different definitions of vertexes and edges to describe the structure of proteins. Protein folds into a specific conformation for its function depending on interactions between residues. Consequently, in many studies, a protein structure was treated as a complex system comprised of individual components residues, and edges were interactions between residues. What is the proper time for representing a protein structure as a network? To confirm the effect of different definitions of vertexes and edges in constructing the amino acid interaction networks, protein domains and the structural unit of proteins were described using this method. The identification performance of 2847 proteins with domain/domains proved that the structure of proteins was described well when was around 5.0–7.5 Å, and the optimal cutoff value for constructing the protein structure networks was 5.0 Å ( distances) while the ideal community division method was community structure detection based on edge betweenness in this study.