SimDiv: A New Solution for Protein Comparison

  • Hassan Sayyadi
  • Sara Salehi
  • Mohammad Ghodsi
Part of the Lecture Notes in Electrical Engineering book series (LNEE, volume 6)

The number of known proteins is increasing every day; tens of thousands have been studied and categorized by now.

In this chapter, we propose a model for protein matching or extracting similar parts of two given proteins. We focus on the computational geometric approach and the graph matching method that are used to model and compare the sequence and 3D structure of proteins.

The remainder of this chapter is organized as follows. We first have a glance at the related works. There are two major methods used in the literature: Delaunay tetrahedralization and similarity flooding.We explain the required information in the next section as background knowledge, and then propose a new idea in Sect. 33.4 which can improve the current methods.We then present experimental results of the implemented method which show its effectiveness.


Voronoi Diagram Similar Part Similar Component Protein Comparison Delaunay Tessellation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Eidhammer I, Jonasses I, Taylor W (2000) Structure comparison and structure patterns. Journal of Computational Biology. Volume 7. 685–716CrossRefGoogle Scholar
  2. 2.
    Finney J (1970) Random packing and the structure of simple liquids, the geometry of the random close packing. Proceedings of the Royal Society. Volume 319. 479–493CrossRefGoogle Scholar
  3. 3.
    Tropsha A, Carter C, Cammer S, Vaisman I (2003) Simplicial neighborhood analysis of protein packing (SNAPP): A computational geometry approach to studying proteins. Methods in Enzymology. Volume 374. 509–544CrossRefGoogle Scholar
  4. 4.
    Cho W Z S, Vaisman I, Tropsha A (1997) A new approach to protein fold recognition based on delaunay tessellation of protein structure. In: Pacific Symposium on Biocomputing, Singapore 487–496Google Scholar
  5. 5.
    Carter C, LeFebvre B, Cammer S, Trosha A, Edgell M (2001) Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations. Journal of Molecular Biology. Volume 311. No. 4. 625–638CrossRefGoogle Scholar
  6. 6.
    Roach J, Sharma S, Kapustina M, Carter C (2005) Structure alignment via delaunay tetrahedralization. Proteins: Structure, Function, and Bioinformatics. Volume 60. 66–81CrossRefGoogle Scholar
  7. 7.
    Bostick D, Shen M, Vaisman I (2004) A simple topological representation of protein structure: Implications for new, fast, and robust structural classification. Proteins: Structure, Function, and Bioinformatics. Volume 56. 487–501CrossRefGoogle Scholar
  8. 8.
    Hun J, Bandyopadhyay D, Wang W, Snoeyink J, Prins J, Trosha A (2005) Comparing graph representations of protein structure for mining family-specific residue-based packing motifs. Journal of Computational Biology. Volume 12. 657–671CrossRefGoogle Scholar
  9. 9.
    Dafas P, Gomoluch A K, Schroeder M (2004) Structural protein interactions: From months to minutes. In: Elsevier B.V, Parallel Computing: Software Technology, Algorithms, Architectures & Applications. 677–684Google Scholar
  10. 10.
    Park J, Lappe M, Teichmann S A (2001) Mapping protein family interactions: Intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. Journal of Molecular Biology. Volume 307. No. 3. 929–938CrossRefGoogle Scholar
  11. 11.
  12. 12.
    Garcia-Molina S M H, Rahm E (2002) Similarity flooding: A versatile graph matching algorithm and its application to schema matching. In: Proceedings of the 18th International Conference on Data Engineering (ICDE), San Jose, CAGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Hassan Sayyadi
    • 1
  • Sara Salehi
    • 2
  • Mohammad Ghodsi
    • 1
    • 3
  1. 1.Computer Engineering DepartmentSharif University of TechnologyTehranIran
  2. 2.Computer Engineering DepartmentAzad University, Tehran-South BranchIran
  3. 3.IPM School of Computer ScienceTehranIran

Personalised recommendations