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Scalable System for Protein Structure Similarity Searching

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Computational Collective Intelligence. Technologies and Applications (ICCCI 2011)

Abstract

One of the advantages of using multi-agent systems in solving many problems is their high scalability adequately to the demand for computing power. This important feature underlies our agent-based system for protein structure similarity searching. In this paper, we present the general architecture of the system, implementation details, communication between agents, distribution of databases, and user interface. Moreover, presented results of numerical experiments show that distributing the computational procedure across multiple computers results in significant acceleration of the search process.

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References

  1. Lodish, H., Berk, A., Zipursky, S.L., et al.: Molecular Cell Biology, 4th edn. W. H. Freeman and Company, NY (2001)

    Google Scholar 

  2. Branden, C., Tooze, J.: Introduction to Protein Structure. Garland, New York (1991)

    Google Scholar 

  3. Gibrat, J.F., Madej, T., Bryant, S.H.: Surprising similarities in structure comparison. Curr. Opin. Struct. Biol. 6(3), 377–385 (1996)

    Article  Google Scholar 

  4. Holm, L., Sander, C.: Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233(1), 123–138 (1993)

    Article  Google Scholar 

  5. Shindyalov, I.N., Bourne, P.E.: Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein. Eng. 11(9), 739–747 (1998)

    Article  Google Scholar 

  6. Friedberg, I., et al.: Using an alignment of fragment strings for comparing protein structures. Bioinformatics 23(2), 219–224 (2007)

    Article  Google Scholar 

  7. Berman, H.M., et al.: The Protein Data Bank. Nucleic Acids Res. 28, 235–242 (2000)

    Article  Google Scholar 

  8. Momot, A., Małysiak-Mrozek, B., Kozielski, S., Mrozek, D., Hera, Ł., Górczyńska-Kosiorz, S., Momot, M.: Improving Performance of Protein Structure Similarity Searching by Distributing Computations in Hierarchical Multi-Agent System. In: Pan, J.-S., Chen, S.-M., Nguyen, N.T. (eds.) ICCCI 2010. LNCS (LNAI), vol. 6421, pp. 320–329. Springer, Heidelberg (2010)

    Chapter  Google Scholar 

  9. Folino, G., et al.: Towards a Distributed Framework for Protein (Structure) Comparison, Knowledge, Similarity and Information (ProCKSI). In: UK eScience All Hands Meeting (AHM-2008), Edinburgh, UK, pp. 1–2 (2008)

    Google Scholar 

  10. Bellifemine, F., et al.: JADE, A White Paper (2003), http://jade.tilab.com/papers/2003/WhitePaperJADEEXP.pdf

  11. Franklin, S., Graesser, A.: Is it an Agent, or just a Program?: A Taxonomy for Autonomous Agents. In: Jennings, N.R., Wooldridge, M.J., Müller, J.P. (eds.) ECAI-WS 1996 and ATAL 1996. LNCS, vol. 1193, pp. 21–35. Springer, Heidelberg (1997)

    Chapter  Google Scholar 

  12. Wobcke, W., Pagnuccco, M., Zhang, C. (eds.): Agents and Multi-Agent Systems Formalisms, Methodologies, and Applications. LNCS (LNAI), vol. 1441. Springer, Heidelberg (1998)

    Google Scholar 

  13. Jain, L.C., Chen, Z., Ichalkaranje, N. (eds.): Intelligent agents and their applications. Physica, Heidelberg (2002)

    MATH  Google Scholar 

  14. Ghose, A., Governatori, G., Sadananda, R. (eds.): PRIMA 2007. LNCS (LNAI), vol. 5044. Springer, Heidelberg (2009)

    MATH  Google Scholar 

  15. Jennings, N.R., Sycara, K., Wooldridge, M.: A roadmap of agent research and development. Autonomous Agents and Multi-Agent Systems 1, 7–38 (1998)

    Article  Google Scholar 

  16. Richards, N., Griffith, S.: JBoss: A Developer’s Notebook. O’Reilly, Sebastopol (2005)

    Google Scholar 

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Małysiak-Mrozek, B., Momot, A., Mrozek, D., Hera, Ł., Kozielski, S., Momot, M. (2011). Scalable System for Protein Structure Similarity Searching. In: Jędrzejowicz, P., Nguyen, N.T., Hoang, K. (eds) Computational Collective Intelligence. Technologies and Applications. ICCCI 2011. Lecture Notes in Computer Science(), vol 6923. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-23938-0_28

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  • DOI: https://doi.org/10.1007/978-3-642-23938-0_28

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-23937-3

  • Online ISBN: 978-3-642-23938-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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