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Discrimination of proteins using graph theoretic properties

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Graph theoretic properties of proteins can be used to perceive the differences between correctly folded proteins and well designed decoy sets. Graphs are used to represent 3D protein structures. We used two different graph representations of protein structures which are Delaunay tessellations of proteins and contact map graphs. Graph theoretic properties for both graph types showed high classification accuracy to discrimination of proteins. Different type of linear classifiers and support vector classifier were used to classification of the protein structures. The best classifier accuracy was over 95% as shown in Table 1. The results showed that characteristic features of graph theoretic properties can be used many fields such as prediction of fold recognition, structure alignment and comparison, detection of similar domains and definition of structural motifs in high accuracy.

Table 1 :


In this work we successfully showed that structural properties as well as potential scores can be used to discriminate native folds from the decoy sets. As far as graph types are concerned, the classification accuracy rates of the results obtained from contact map graphs are higher than the results obtained from Delaunay tessellated graphs for the same classification methods. Therefore contact map matrices are better representation method for protein structures. Support vector classifier and quadratic classifiers results are quite promising for the dataset which formed after outlier analysis. The accuracy rates are over 95%.


  1. 1.

    Strogatz SH: Exploring Complex Networks. 2001, 410: 268-276.

  2. 2.

    Albert R, Barabasi A-L: Statistical mechanics of complex networks. Rev Mod Phys. 2002, 74: 47-97. 10.1103/RevModPhys.74.47.

  3. 3.

    McConkey BJ, Sobolev V, Eldman M: Discrimination of native protein structures using atom-atom contact scoring. Proc Natl Acad Sci. 2003, 100: 3215-3220. 10.1073/pnas.0535768100

  4. 4.

    Wang K, Fain B, Levitt M, Samudrala R: Improved protein structure selection using decoy-dependent discriminatory functions. BMC Struct Biol. 2004, 4: 8- 10.1186/1472-6807-4-8

  5. 5.

    Taylor T, Vaisman II: Graph theoretic properties of networks formed by the Delaunay tessellation of protein structures. Phys Rev E Stat Nonlin Soft Matter Phys. 2006, 73: 041925-

  6. 6.

    Alper Küçükural, Uğur Sezerman: Finding Common Domains of Proteins Using Parallelized Attributed Inexact Sub-graph Matching Algorithm. TAM. 2006

  7. 7.

    Miyazawa S, Jernigan RL: J Mol Biol. 1996, 256: 623-644. 10.1006/jmbi.1996.0114

  8. 8.

    Liang J, Dill KA: Are proteins Well-Packed?. Biophys J. 2001, 81: 751-766. 10.1016/S0006-3495(01)75739-6

  9. 9.

    Atilgan AR, Akan P, Baysal C: "Small-World Communication of Residues and Significance for Protein Dynamics, ". Biophys J. 2004, 86: 85-91. 10.1016/S0006-3495(04)74086-2

  10. 10.

    Vendruscolo M, Kussel E, Domany E: Recovery of Protein Structure from Contact Maps. Fold Des. 1997, 2: 295-306. 10.1016/S1359-0278(97)00041-2

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Correspondence to Alper Küçükural.

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Open Access This article is published under license to BioMed Central Ltd. This is an Open Access article is distributed under the terms of the Creative Commons Attribution 2.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Küçükural, A., Sezerman, O.U. Discrimination of proteins using graph theoretic properties. BMC Syst Biol 1, P49 (2007) doi:10.1186/1752-0509-1-S1-P49

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  • Classification Accuracy
  • Accuracy Rate
  • Structure Alignment
  • Classifier Accuracy
  • Linear Classifier