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Graph Comparison by Log-Odds Score Matrices with Application to Protein Topology Analysis
March/April 2011 (vol. 8 no. 2)
pp. 564-569
J. Rocha, University of the Balearic Islands, Palma
A TOPS diagram is a simplified description of the topology of a protein using a graph where nodes are \alpha-helices and \beta-strands, and edges correspond to chirality relations and parallel or antiparallel bonds between strands. We present a matching algorithm between two TOPS diagrams where the likelihood of a match is measured according to previously known matches between complete 3D structures. This totally new 3D training is recorded on transition matrices that count the likelihood that a given TOPS feature, or combination thereof, is replaced by another feature on homologs. The new algorithm outperforms existing ones on a benchmark database. Some biologically significant examples are discussed as well. The method can be used whenever frequencies of edge relationship matches are known, as it is the case for several biopolymer structures.

[1] A. Kouranov, L. Xie, J. de la Cruz, L. Chen, J. Westbrook, P.E. Bourne, and H.M. Berman, "The RCSB PDB Information Portal for Structural Genomics," Nucleic Acids Research, vol. 34, pp. D302-D305, 2006.
[2] S.K. Burley, S.C. Almo, J.B. Bonanno, M. Capel, M.R. Chance, T. Gaasterland, D. Lin, A.S. Caronali, F.W. Studier, and S. Swaminathan, "Structural Genomics: Beyond the Human Genome Project," Nature Genetics, vol. 23, no. 2, pp. 151-157, 1999.
[3] S.-H. Kim, "Shining a Light on Structural Genomics," Nature Structural Biology, vol. 5, pp. 643-645, 1998.
[4] T. Flores, D. Moss, and J. Thornton, "An Algorithm for Automatically Generating Protein Topology Cartoons," Protein Eng., vol. 7, no. 1, pp. 31-37, 1994.
[5] D.R. Gilbert, D.R. Westhead, N. Nagano, and J.M. Thornton, "Motif-Based Searching in Tops Protein Topology Databases," Bioinformatics, vol. 15, no. 4, pp. 317-326, 1999.
[6] D.R. Westhead, D.C. Hutton, and J.M. Thornton, "An Atlas of Protein Topology Cartoons Available on the World Wide Web," Trends in Biochemical Science, vol. 23, no. 1, pp. 35-36, 1998.
[7] D.R. Westhead, T. Slidel, T. Flores, and J.M. Thornton, "Protein Structural Topology: Automated Analysis and Diagrammatic Representations," Protein Science, vol. 8, no. 4, pp. 897-904, 1999.
[8] T. Madej, J.F. Gibrat, and S.H. Bryant, "Threading a Database of Protein Cores," Proteins, vol. 23, no. 3, pp. 356-369, 1995.
[9] T. Madej and M.C. Mossing, "Hamiltonians for Protein Tertiary Structure Prediction Based on Three-Dimensional Environment Principles," J. Molecular Biology, vol. 233, no. 3, pp. 480-487, 1993.
[10] I. Koch, T. Lengauer, and E. Wanke, "An Algorithm for Finding Maximal Common Subtopologies in a Set of Protein Structures," J. Computational Biology, vol. 3, no. 2, pp. 289-306, 1996.
[11] T. Kawabata and K. Nishikawa, "Protein Structure Comparison Using the Markov Transition Model of Evolution," Proteins, vol. 41, pp. 108-122, 2000.
[12] E. Krissinel and K. Henrick, "Secondary-Structure Matching (SSM), a New Tool for Fast Protein Structure Alignment in Three Dimensions," Acta Crystallographica, vol. D60, pp. 2256-2268, 2004.
[13] J. Viksna and D. Gilbert, "Assessment of the Probabilities for Evolutionary Structural Changes in Protein Folds," Bioinformatics, vol. 23, no. 7, pp. 832-841, 2007.
[14] J. Viksna et al., "Protein Structure Comparison Based on Profiles of Topological Motifs: A Feasible Way to Deal with Information from Negative Examples," Proc. German Bioinformatics Conf., pp. 159-165, 2003.
[15] G.M. Torrance, D.R. Gilbert, I. Michalopoulos, and D.W. Westhead, "Protein Structure Topological Comparison, Discovery and Matching Service," Bioinformatics, vol. 21, no. 10, pp. 2537-2538, 2005.
[16] J. Viksna and D. Gilbert, "Pattern Matching and Pattern Discovery Algorithms for Protein Topologies," Proc. Int'l Workshop Algorithms Bioinformatics (WABI), pp. 98-111, 2001.
[17] K. Mizuguchi and N. Go, "Comparison of Spatial Arrangements of Secondary Structure Elements in Proteins," Protein Eng., vol. 8, pp. 353-362, 1995.
[18] D. Gilbert, D. Westhead, J. Viksna, and J. Thornton, "A Computer System to Perform Structure Comparison Using TOPS Representations of Protein Structure," J. Computational Chemistry, vol. 26, no. 1, pp. 23-30, 2001.
[19] J. Chandonia, G. Hon, N. Walker, L. Lo Conte, P. Koehl, M. Levitt, and S. Brenner, "The Astral Compendium in 2004," Nucleic Acids Research, vol. 32, pp. 189-192, 2004.
[20] R. Durbin, S.R. Eddy, A. Krogh, and G. Mitchison, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, seventh ed. Cambridge Univ. Press, 2002.
[21] M. Sierk and W. Pearson, "Sensitivity and Selectivity in Protein Structure Comparison," Protein Science, vol. 13, pp. 773-785, 2004.
[22] C. Orengo et al., "CATH: A Hierarchic Classification of Protein Domain Structures," Structure, vol. 5, pp. 1093-1108, 1997.
[23] J. Rocha, J. Segura, R. Wilson, and S. Dasgupta, "Flexible Structural Protein Alignment by a Sequence of Local Transformations," Bioinformatics, vol. 25, pp. 1625-1631, 2009.

Index Terms:
TOPS diagrams, BLOSUM matrices, secondary structure alignment, MatTops, graph matching.
J. Rocha, "Graph Comparison by Log-Odds Score Matrices with Application to Protein Topology Analysis," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 2, pp. 564-569, March-April 2011, doi:10.1109/TCBB.2010.59
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