Abstract
This paper proposes a novel fast protein structure alignment algorithm and its application. Because it is known that the functions of protein are derived from its structure, the method of measuring the structural similarities between two proteins can be used to infer their functional closeness. In this paper, we propose a 3D chain code representation for fast measuring the local geometric similarity of protein and introduce a backtracking algorithm for joining a similar local substructure efficiently. A 3D chain code, which is a sequence of the directional vectors between the atoms in a protein, represents a local similarity of protein. After constructing a pair of similar substructures by referencing local similarity, we perform the protein alignment by joining the similar substructure pair through a backtracking algorithm. This method has particular advantages over all previous approaches; our 3D chain code representation is more intuitive and our experiments prove that the backtracking algorithm is faster than dynamic programming in general case. We have designed and implemented a protein structure alignment system based on our protein visualization software (MoleView). These experiments show rapid alignment with precise results.
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References
Bourne, P.E., Weissig, H.: Structural Bioinformatics. Wiley-Liss, Chichester (2003)
Taylor, W., Orengo, C.: Protein structure alignment. Journal of Molecular Biology 208, 1–22 (1989)
Holm, L., Sander, C.: Protein Structure Comparison by alignment of distance matrices. Journal of Molecular Biology 233, 123–138 (1993)
Schwarzer, R., Lotan, I.: Approximation of Protein Structure for Fast Similarity Measures. In: Proc. 7th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pp. 267–276 (2003)
Singh, A.P., Brutlag, D.L.: Hierarchical Protein Structure Superposition using both Secondary Structure and Atomic Representation. In: Proc. Intelligent Systems for Molecular Biology (1993)
Won, C.S., Park, D.K., Park, S.J.: Efficient use of MPEG-7 Edge Histogram Descriptor. ETRI Journal 24(1), 22–30 (2002)
Shindyalov, I.N., Bourne, P.E.: Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 11, 739–747 (1993)
Databases and Tools for 3-D protein Structure Comparison and Alignment Using the Combinatorial Extension (CE) Method, http://cl.sdsc.edu/ce.html
Park, C., et al.: MoleView: A program for molecular visualization. In: Genome Informatics 2004, p. 167-1 (2004)
Lamdan, Y., Wolfson, H.J.: Geometric hashing: a general and efficient model-based recognition scheme. In: Proc. of the 2nd International Conference on ComputerVision (ICCV), pp. 238–249 (1988)
Leibowitz, N., Fligelman, Z.Y., Nussinov, R., Wolfson, H.J.: Multiple Structural Alignment and Core Detection by Geometric Hashing. In: Proc. of the 7th International Conference on Intelligent Systems for Molecular Biology (ISMB), pp. 169–177 (1999)
Nussinov, R., Wolfson, H.J.: Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Biophysics 88, 10495–10499 (1991)
Pennec, X., Ayache, N.: A geometric algorithm to find small but highly similar 3D substructures in proteins. Bioinformatics 14(6), 516–522 (1998)
Holm, L., Sander, C.: Protein Structure Comparison by Alignment of Distance Matrices. Journal of Molecular Biology 233(1), 123–138 (1993)
Golomb, S., Baumert, L.: Backtrack programming. J. ACM 12, 516–524 (1965)
Gans, J., Shalloway, D., Qmol, A.: program for molecular visualization on Windows based PCs. Journal of Molecular Graphics and Modelling 19, 557–559 (2001)
Bribiesca, E.: A chain code for representing 3D curves. Pattern Recognition 33, 755–765 (2000)
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Park, CY. et al. (2006). Fast Protein Structure Alignment Algorithm Based on Local Geometric Similarity. In: Gelbukh, A., Reyes-Garcia, C.A. (eds) MICAI 2006: Advances in Artificial Intelligence. MICAI 2006. Lecture Notes in Computer Science(), vol 4293. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11925231_113
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DOI: https://doi.org/10.1007/11925231_113
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