Improving performance of protein structure similarity searching by distributing computations in hierarchical multi-agent system

Alina Momot; Bozena Małysiak-Mrozek; Stanisław Kozielski; Dariusz Mrozek; Łukasz Hera; Sylwia Górczyńska-Kosiorz; Michał Momot

doi:10.1007/978-3-642-16693-8_34

Improving performance of protein structure similarity searching by distributing computations in hierarchical multi-agent system

Alina Momot
, Bozena Małysiak-Mrozek
, Stanisław Kozielski
, Dariusz Mrozek
, Łukasz Hera
, Sylwia Górczyńska-Kosiorz
, Michał Momot

Silesian University of Technology
Medical University of Silesia in Katowice
Institute of Medical Technology and Equipment

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

13 Citations (Scopus)

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.

Original language	English
Title of host publication	Computational Collective Intelligence
Subtitle of host publication	Technologies and Applications - Second International Conference, ICCCI 2010, Proceedings
Pages	320-329
Number of pages	10
Edition	PART 1
DOIs	https://doi.org/10.1007/978-3-642-16693-8_34
Publication status	Published - 2010
Event	2nd International Conference on Computational Collective Intelligence - Technologies and Applications, ICCCI 2010 - Kaohsiung, Taiwan, Province of China Duration: 10 Nov 2010 → 12 Nov 2010

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Number	PART 1
Volume	6421 LNAI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	2nd International Conference on Computational Collective Intelligence - Technologies and Applications, ICCCI 2010
Country/Territory	Taiwan, Province of China
City	Kaohsiung
Period	10/11/10 → 12/11/10

Keywords

Distributed computing
Multi-agent system
Protein structure
Proteins
Similarity searching

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-642-16693-8_34

Cite this

Momot, A., Małysiak-Mrozek, B., Kozielski, S., Mrozek, D., Hera, Ł., Górczyńska-Kosiorz, S., & Momot, M. (2010). Improving performance of protein structure similarity searching by distributing computations in hierarchical multi-agent system. In Computational Collective Intelligence: Technologies and Applications - Second International Conference, ICCCI 2010, Proceedings (PART 1 ed., pp. 320-329). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6421 LNAI, No. PART 1). https://doi.org/10.1007/978-3-642-16693-8_34

Momot, Alina ; Małysiak-Mrozek, Bozena ; Kozielski, Stanisław et al. / Improving performance of protein structure similarity searching by distributing computations in hierarchical multi-agent system. Computational Collective Intelligence: Technologies and Applications - Second International Conference, ICCCI 2010, Proceedings. PART 1. ed. 2010. pp. 320-329 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); PART 1).

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title = "Improving performance of protein structure similarity searching by distributing computations in hierarchical multi-agent system",

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.",

keywords = "Distributed computing, Multi-agent system, Protein structure, Proteins, Similarity searching",

author = "Alina Momot and Bozena Ma{\l}ysiak-Mrozek and Stanis{\l}aw Kozielski and Dariusz Mrozek and {\L}ukasz Hera and Sylwia G{\'o}rczy{\'n}ska-Kosiorz and Micha{\l} Momot",

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doi = "10.1007/978-3-642-16693-8\_34",

language = "English",

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series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

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Momot, A , Małysiak-Mrozek, B, Kozielski, S, Mrozek, D, Hera, Ł, Górczyńska-Kosiorz, S & Momot, M 2010, Improving performance of protein structure similarity searching by distributing computations in hierarchical multi-agent system. in Computational Collective Intelligence: Technologies and Applications - Second International Conference, ICCCI 2010, Proceedings. PART 1 edn, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), no. PART 1, vol. 6421 LNAI, pp. 320-329, 2nd International Conference on Computational Collective Intelligence - Technologies and Applications, ICCCI 2010, Kaohsiung, Taiwan, Province of China, 10/11/10. https://doi.org/10.1007/978-3-642-16693-8_34

Improving performance of protein structure similarity searching by distributing computations in hierarchical multi-agent system. / Momot, Alina ; Małysiak-Mrozek, Bozena; Kozielski, Stanisław et al.
Computational Collective Intelligence: Technologies and Applications - Second International Conference, ICCCI 2010, Proceedings. PART 1. ed. 2010. p. 320-329 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6421 LNAI, No. PART 1).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AU - Momot, Alina

AU - Małysiak-Mrozek, Bozena

AU - Kozielski, Stanisław

AU - Mrozek, Dariusz

AU - Hera, Łukasz

AU - Górczyńska-Kosiorz, Sylwia

AU - Momot, Michał

PY - 2010

Y1 - 2010

N2 - 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.

AB - 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.

KW - Distributed computing

KW - Multi-agent system

KW - Protein structure

KW - Proteins

KW - Similarity searching

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SN - 9783642166921

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 320

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Y2 - 10 November 2010 through 12 November 2010

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Momot A , Małysiak-Mrozek B, Kozielski S, Mrozek D, Hera Ł, Górczyńska-Kosiorz S et al. Improving performance of protein structure similarity searching by distributing computations in hierarchical multi-agent system. In Computational Collective Intelligence: Technologies and Applications - Second International Conference, ICCCI 2010, Proceedings. PART 1 ed. 2010. p. 320-329. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); PART 1). doi: 10.1007/978-3-642-16693-8_34

Improving performance of protein structure similarity searching by distributing computations in hierarchical multi-agent system

Abstract

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Keywords

ASJC Scopus subject areas

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