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Improving Performance of Protein Structure Similarity Searching by Distributing Computations in Hierarchical Multi-Agent System

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Computational Collective Intelligence. Technologies and Applications (ICCCI 2010)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 6421))

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Abstract

Since protein structure similarity searching is very complex and time-consuming, one of the possible acceleration methods is parallelization by distributing the calculation on multiple computers. In the paper, we present a theoretical model of the hierarchical multi-agent system dedicated to the task of protein structure similarity searching. We also show results of several numerical experiments confirming a suitability of such distribution for the similarity searching performed for the Muconate Lactonizing Enzyme (PDB ID = 1MUC) from the Protein Data Bank (PDB) against the database containing almost thousand randomly chosen molecules.

Scientific research supported by the Ministry of Science and Higher Education, Poland in years 2008-2010, Grant No. N N516 265835: Protein Structure Similarity Searching in Distributed Multi Agent System.

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Authors and Affiliations

  1. Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland

    Alina Momot, Bożena Małysiak-Mrozek, Stanisław Kozielski, Dariusz Mrozek & Łukasz Hera

  2. Clinical Department of Nephrology, Diabetology and Internal Diseases, Medical University of Silesia, Poniatowskiego 15, Katowice, Poland

    Sylwia Górczyńska-Kosiorz

  3. Institute of Medical Technology and Equipment, Roosevelta 118, 41-800, Zabrze, Poland

    Michał Momot

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  1. Alina Momot
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  3. Stanisław Kozielski
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Editors and Affiliations

  1. Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, 415 Chien-Kung Road, 807, Kaohsiung, Taiwan

    Jeng-Shyang Pan

  2. Department of Computer Science and Information Engineering, National Taiwan University of Science and Technology, #43, Sec.4, Keelung Rd., 106, Taipei, Taiwan

    Shyi-Ming Chen

  3. Institute of Informatics, Wroclaw University of Technology, Str. Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland

    Ngoc Thanh Nguyen

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Momot, A. et al. (2010). Improving Performance of Protein Structure Similarity Searching by Distributing Computations in Hierarchical Multi-Agent System. In: Pan, JS., Chen, SM., Nguyen, N.T. (eds) Computational Collective Intelligence. Technologies and Applications. ICCCI 2010. Lecture Notes in Computer Science(), vol 6421. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16693-8_34

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  • DOI: https://doi.org/10.1007/978-3-642-16693-8_34

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-16692-1

  • Online ISBN: 978-3-642-16693-8

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