Paper Info
Title
The effect of edge definition of complex networks on protein structure identification.
Abstract
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 R-C alpha was around 5.0-7.5 angstrom, and the optimal cutoff value for constructing the protein structure networks was 5.0 angstrom (C-alpha-C-alpha distances) while the ideal community division method was community structure detection based on edge betweenness in this study.
Year
DOI
Venue
2013
10.1155/2013/365410
COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE
Keywords
DocType
Volume
protein conformation,computational biology,proteins,amino acids,algorithms
Journal
2013
Issue
ISSN
Citations 
null
1748-670X
1
PageRank 
References 
Authors
0.35
19
6
Name
Order
Citations
PageRank
Jing Sun110.35
Runyu Jing231.42
Di Wu3636117.73
Tuanfei Zhu430.74
Menglong Li59411.85
Yizhou Li6694.70