Network properties of protein structures

2004/08/13 by Ganesh Bagler, Somdatta Sinha · 155 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Computer Science · #Artificial intelligence #Biochemistry #Bioinformatics and Genomic Networks #Biology #Chemistry #Class (philosophy) #Complex network #Computational Drug Discovery Methods #Computational biology #Computer science #Genetics #Modularity (biology) #Network structure #Perspective (graphical) #Protein Structure and Dynamics #Protein structure #Theoretical computer science #q-bio.BM #q-bio.MN

paper · pdf · doi:10.1016/j.physa.2004.08.046

published in Physica A Statistical Mechanics and its Applications 346(1-2), 27-33 (Elsevier BV) · 5 pages, 7 postscript figures, Accepted for publication in Physica A

arxiv created 2004/08/13 · openalex publication_date 2004/09/18 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05

Abstract

Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show small-world network property. Various network parameters offer insight into the structural organisation of proteins and provide indications of modularity in protein networks.

Citations

• Emergence of scaling in random networks
• Statistical mechanics of complex networks
• The large-scale organization of metabolic networks

Cited by

• Assortative mixing in Protein Contact Networks and protein folding kinetics
• Analysis of heat kernel highlights the strongly modular and heat-preserving structure of proteins