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Network properties of protein structures

Author

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  • Bagler, Ganesh
  • Sinha, Somdatta

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.

Suggested Citation

  • Bagler, Ganesh & Sinha, Somdatta, 2005. "Network properties of protein structures," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 346(1), pages 27-33.
    • Handle: RePEc:eee:phsmap:v:346:y:2005:i:1:p:27-33
    DOI: 10.1016/j.physa.2004.08.046
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    Citations

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    Cited by:

    1. Livi, Lorenzo & Maiorino, Enrico & Pinna, Andrea & Sadeghian, Alireza & Rizzi, Antonello & Giuliani, Alessandro, 2016. "Analysis of heat kernel highlights the strongly modular and heat-preserving structure of proteins," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 441(C), pages 199-214.
    2. Emerson, Isaac Arnold & Amala, Arumugam, 2017. "Protein contact maps: A binary depiction of protein 3D structures," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 465(C), pages 782-791.
    3. Alves, Nelson Augusto & Martinez, Alexandre Souto, 2007. "Inferring topological features of proteins from amino acid residue networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 375(1), pages 336-344.
    4. Emerson, I. Arnold & Gothandam, K.M., 2012. "Network analysis of transmembrane protein structures," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 391(3), pages 905-916.
    5. Zhou, Yuan-Wu & Liu, Jin-Long & Yu, Zu-Guo & Zhao, Zhi-Qin & Anh, Vo, 2014. "Fractal and complex network analyses of protein molecular dynamics," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 416(C), pages 21-32.
    6. Guo-Ling Jia & Rong-Guo Ma & Zhi-Hua Hu, 2019. "Urban Transit Network Properties Evaluation and Optimization Based on Complex Network Theory," Sustainability, MDPI, vol. 11(7), pages 1-16, April.
    7. Srivastava, Divyanshu & Bagler, Ganesh & Kumar, Vibhor, 2023. "Graph Signal Processing on protein residue networks helps in studying its biophysical properties," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 615(C).

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