Abstract
Searching for similar proteins through the comparison of their spatial structures requires efficient and fully automated methods and become an area of dynamic researches in recent years. We developed an algorithm and set of tools called EAST (Energy Alignment Search Tool). The EAST serves as a tool for finding strong protein structural similarities in a database of protein structures. The similarity searching is performed through the comparison and alignment of protein energy profiles received in the computational process based on the molecular mechanics theory. This representation of protein structures reduces the huge search space. In order to accelerate presented method we implemented it with the use of Multi Agent System (MAS). This significantly improved the efficiency of the search process. In the paper, we present the complexity of the search process, the main idea of the EAST algorithm and brief discussion on the advantages of its implementation as MAS.
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References
Fersht, A.: Enzyme Structure and Mechanism, 2nd edn. W.H. Freeman & Co., NY (1985)
Dickerson, R.E., Geis, I.: The Structure and Action of Proteins, 2nd edn. Benjamin/Cummings, Redwood City (1981)
Lodish, H., Berk, A., Zipursky, S.L., et al.: Molecular Cell Biology, 4th edn. W. H. Freeman and Company, NY (2001)
Branden, C., Tooze, J.: Introduction to Protein Structure. Garland (1991)
Creighton, T.E.: Proteins: Structures and molecular properties. Freeman, San Fransico (1993)
Gibrat, J.F., Madej, T., Bryant, S.H.: Surprising similarities in structure comparison. Curr. Opin. Struct. Biol. 6(3), 377–385 (1996)
Holm, L., Sander, C.: Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233(1), 123–138 (1993)
Shindyalov, I.N., Bourne, P.E.: Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering 11(9), 739–747 (1998)
Can, T., Wang, Y.F.: CTSS: A Robust and Efficient Method for Protein Structure Alignment Based on Local Geometrical and Biological Features. In: Proceedings of the 2003 IEEE Bioinformatics Conference (CSB 2003), pp. 169–179 (2003)
Burkert, U., Allinger, N.L.: Molecular Mechanics. American Chemical Society, Washington (1980)
Wooldridge, M.: Introduction to MultiAgent Systems. Wiley &Sons, Chichester (2002)
Mrozek, D., Małysiak, B., Kozielski, S.: EAST: Energy Alignment Search Tool. In: Wang, L., Jiao, L., Shi, G., Li, X., Liu, J. (eds.) FSKD 2006. LNCS, vol. 4223, pp. 696–705. Springer, Heidelberg (2006)
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., et al.: The Protein Data Bank. Nucleic Acids Res. 28, 235–242 (2000)
Ponder, J.: TINKER – Software Tools for Molecular Design, Dept. of Biochemistry & Molecular Biophysics, Washington University, School of Medicine, St. Louis (June 2001)
Cornell, W.D., Cieplak, P., et al.: A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 117, 5179–5197 (1995)
Mrozek, D., Małysiak, B., Kozielski, S.: An Optimal Alignment of Proteins Energy Characteristics with Crisp and Fuzzy Similarity Awards. In: Proc. of the IEEE International Conference on Fuzzy Systems (FUZZ-IEEE), pp. 1508–1513 (2007)
Smith, T.F., Waterman, M.S.: Identification of common molecular Subsequences. J. Mol. Biol. 147, 195–197 (1981)
Gotoh, O.: An Improved Algorithm for Matching Biological Sequences. J. Mol. Biol. 162, 705–708 (1982)
Sellers, P.H.: Pattern recognition in genetic sequences by mismatch density. Bull. Math. Biol. 46, 510–514 (1984)
Altschul, S.F., Erickson, B.W.: Locally optimal subalignments using nonlinear similarity functions. Bull. Math. Biol. 48, 633–660 (1986)
Altschul, S.F., Erickson, B.W.: Optimal sequence alignment using affine gap costs. Bull. Math. Biol. 48(5-6), 603–616 (1986)
Bellifemine, F., Caire, G., Poggi, A., Rimassa, G.: JADE, A White Paper (2003), http://jade.tilab.com/papers/2003/WhitePaperJADEEXP.pdf
Sayle, R., Milner-White, E.J.: RasMol: Biomolecular graphics for all. Trends in Biochemical Sciences (TIBS) 20(9), 374 (1995)
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Mrozek, D., Małysiak, B., Augustyn, W. (2009). Agent-Supported Protein Structure Similarity Searching. In: Ghose, A., Governatori, G., Sadananda, R. (eds) Agent Computing and Multi-Agent Systems. PRIMA 2007. Lecture Notes in Computer Science(), vol 5044. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-01639-4_5
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DOI: https://doi.org/10.1007/978-3-642-01639-4_5
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