Abstract
It is known that the function of a protein is determined by its structure. Thus, structural similarity between proteins plays an important role as a good predictor of functional similarity. Many methods focus on solving the protein structure alignment problem. In this paper, we propose a graph-based approach to measure the similarity of two proteins. We first transfer a protein into a labeled graph according to its secondary structures, chemical properties, and 3D topology. For two graphs, we then find their maximum common edge subgraph for measuring the structural similarity of the corresponding proteins. By using a practical technique, the maximum common edge subgraph of two graphs can be found efficiently. Finally, by a backtracking, we can find the common substructure of the given proteins. Experimental results show that our method outperforms the RMSD method. This graph-based approach provides a practical direction for measuring protein structural similarity.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. Journal of Molecular Biology 215, 403–410 (1990)
Barrow, H.G., Burstall, R.M.: Subgraph isomorphism, matching relational structures and maximal cliques. Information Processing Letters 4, 83–84 (1976)
Berman, H.M., Westbrook, J., Feng, Z., et al.: The protein data bank. Nucl. Acids Res. 28, 235–242 (2000)
Borgwardt, K.M., Ong, C.S., Schönauer, S., et al.: Protein function prediction via graph kernels. Bioinformatics 21, 47–56 (2005)
Chen, Y.-R., Peng, S.-L., Tsay, Y.-W.: Protein secondary structure prediction based on ramachandran maps. In: Huang, D.-S., Wunsch II, D.C., Levine, D.S., Jo, K.-H. (eds.) ICIC 2008. LNCS, vol. 5226, pp. 204–211. Springer, Heidelberg (2008)
Conte, L.L., Brenner, S.E., Hubbard, T.J.P., Chothia, C., Murzin, A.G.: Scop database in 2002: refinements accommodate structural genomics. Nucl. Acids Res. 30, 264–267 (2002)
Creighton, T.E.: Proteins: structures and molecular properties. W. H. Freeman & Co., New York (1993)
Gan, H.H., Perlow, R.A., Roy, S., et al.: Analysis of protein sequence/structure similarity relationships. Biophysical 83, 2781–2791 (2002)
Garey, M.R., Johnson, D.S.: Computers and Intractability; A Guide to the Theory of NP-Completeness. W. H. Freeman & Co., New York (1990)
Johnson, M.: Relating metrics, lines and variables defined on graphs to problems in medicinal chemistry. In: Alavi, Y., et al. (eds.) Graph theory with applications to algorithms and computer science, pp. 457–470 (1985)
Lesk, A.M.: Detection of three-dimensional patterns of atoms in chemical structures. ACM Commun. 22, 219–224 (1979)
Levi, G.: A note on the derivation of maximal common subgraphs of two directed or undirected graphs. Calcolo 9, 341–352 (1973)
Pardalos, P.M., Rodgers, G.P.: A branch and bound algorithm for the maximum clique problem. Computers & Oper. Res. 19, 363–375 (1992)
Pemmaraju, S., Skiena, S.: Computational Discrete Mathematics: Combinatorics and Graph Theory with Mathematica. Cambridge University Press, Cambridge (1990)
Wilson, C.A., Kreychman, J., Gerstein, M.: Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. Journal of Molecular Biology 297, 233–249 (2000)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Peng, SL., Tsay, YW. (2010). Measuring Protein Structural Similarity by Maximum Common Edge Subgraphs. In: Huang, DS., Zhang, X., Reyes García, C.A., Zhang, L. (eds) Advanced Intelligent Computing Theories and Applications. With Aspects of Artificial Intelligence. ICIC 2010. Lecture Notes in Computer Science(), vol 6216. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-14932-0_13
Download citation
DOI: https://doi.org/10.1007/978-3-642-14932-0_13
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-14931-3
Online ISBN: 978-3-642-14932-0
eBook Packages: Computer ScienceComputer Science (R0)