Assessment of Protein-Graph Remodeling via Conformational Graph Entropy

  • Sheng-Lung Peng
  • Yu-Wei Tsay
Conference paper
Part of the Communications in Computer and Information Science book series (CCIS, volume 375)


In this paper, we propose a measurement for protein graph remodeling based on graph entropy. We extend the concept of graph entropy to determine whether a graph is suitable for representing a protein. The experimental results suggest that when this extended graph entropy is applied, it helps a conformational on protein graph modeling. Besides, it also contributes to the protein structural comparison indirectly if a protein graph is solid.


Protein structural similarity Protein graph Graph entropy 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Bunke, H.: Graph Matching: Theoretical Foundations, Algorithms, and Applications. In: Proc. Vision Interface 2000, pp. 82–88 (2000)Google Scholar
  2. 2.
    Gilbert, D., Westhead, D.R., Nagano, N., Thornton, J.M.: Motif-based Searching in TOPS Protein Topology Databases. Bioinformatics 15, 317–326 (1999)CrossRefGoogle Scholar
  3. 3.
    Vishveshwara, S., Brinda, K.V., Kannan, N.: Protein Structure: Insights from Graph Theory. Journal of The Comp. Chem. 1, 187–211 (2002)CrossRefGoogle Scholar
  4. 4.
    Lund, O., Hansen, J., Brunak, S., Bohr, J.: Relationship between Protein Structure and Geometrical Constraints. Protein Science: A Publication of the Protein Society 5, 2217–2225 (1996)CrossRefGoogle Scholar
  5. 5.
    Nelson, D.L., Cox, M.M.: Lehninger Principles of Biochemistry, 4th edn. Freeman (2004)Google Scholar
  6. 6.
    Huan, J., Bandyopadhyay, D., Wang, W., Snoeyink, J., Prins, J., Tropsha, A.: Comparing Graph Representations of Protein Structure for Mining Family-specific Residue-based Packing Motifs. J. Comput. Biol. 12, 657–671 (2005)CrossRefGoogle Scholar
  7. 7.
    Hsu, C.-H., Peng, S.-L., Tsay, Y.-W.: An Improved Algorithm for Protein Structural Comparison based on Graph Theoretical Approach. Chiang Mai Journal of Science 38, 71–81 (2011)MathSciNetGoogle Scholar
  8. 8.
    Canutescu, A.A., Shelenkov, A.A., Dunbrack, R.L.: A Graph-theory Algorithm for Rapid Protein Side-chain Prediction. Protein Sci. 12, 2001–2014 (2003)CrossRefGoogle Scholar
  9. 9.
    Samudrala, R., Moult, J.: A Graph-theoretic Algorithm for Comparative Modeling of Protein Structure. J. Mol. Biol. 279, 279–287 (1998)CrossRefGoogle Scholar
  10. 10.
    Borgwardt, K.M., Ong, C.S., Schonauer, S., Vishwanathan, S.V.N., Smola, A.J., Kriegel, H.-P.: Protein Function Prediction via Graph Kernels. Bioinformatics 21, i47–i56 (2005)Google Scholar
  11. 11.
    Shannon, C.E.: Prediction and Entropy of Printed English. Bell Systems Technical Journal 30, 50–64 (1951)zbMATHGoogle Scholar
  12. 12.
    Chang, R.: Physical Chemistry for the Biosciences. University Science (2005)Google Scholar
  13. 13.
    Simonyi, G.: Graph Entropy: a Survey. Combinatorial Optimization 20, 399–441 (1995)MathSciNetGoogle Scholar
  14. 14.
    Dehmer, M., Emmert-Streib, F.: Structural Information Content of Networks: Graph Entropy based on Local Vertex Functionals. Computational Biology and Chemistry 32, 131–138 (2008)MathSciNetzbMATHCrossRefGoogle Scholar
  15. 15.
    Pamer, E., Cresswell, P.: Mechanisms of MHC Class I – Restricted Antigen Processing. Annual Review of Immunology 16, 323–358 (1998)CrossRefGoogle Scholar
  16. 16.
    Berman, H.M., Westbrook, J., Feng, Z., et al.: The Protein Data Bank, Nucl. Nucl. Acids Res. 28, 235–242 (2000)CrossRefGoogle Scholar
  17. 17.
    Peng, S.-L., Tsay, Y.-W.: On the Usage of Graph Spectra in Protein Structural Similarity. Journal of Computers 23, 95–102 (2012)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Sheng-Lung Peng
    • 1
  • Yu-Wei Tsay
    • 1
  1. 1.Department of Computer Science and Information EngineeringNational Dong Hwa UniversityHualienTaiwan

Personalised recommendations