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Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures
Joint Authors
Sharma, Anuj
Manolakos, Elias S.
Source
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-13, 13 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-10-28
Country of Publication
Egypt
No. of Pages
13
Main Subjects
Abstract EN
Fast increasing computational demand for all-to-all protein structures comparison (PSC) is a result of three confounding factors: rapidly expanding structural proteomics databases, high computational complexity of pairwise protein comparison algorithms, and the trend in the domain towards using multiple criteria for protein structures comparison (MCPSC) and combining results.
We have developed a software framework that exploits many-core and multicore CPUs to implement efficient parallel MCPSC in modern processors based on three popular PSC methods, namely, TMalign, CE, and USM.
We evaluate and compare the performance and efficiency of the two parallel MCPSC implementations using Intel’s experimental many-core Single-Chip Cloud Computer (SCC) as well as Intel’s Core i7 multicore processor.
We show that the 48-core SCC is more efficient than the latest generation Core i7, achieving a speedup factor of 42 (efficiency of 0.9), making many-core processors an exciting emerging technology for large-scale structural proteomics.
We compare and contrast the performance of the two processors on several datasets and also show that MCPSC outperforms its component methods in grouping related domains, achieving a highF-measure of 0.91 on the benchmark CK34 dataset.
The software implementation for protein structure comparison using the three methods and combined MCPSC, along with the developed underlying rckskel algorithmic skeletons library, is available via GitHub.
American Psychological Association (APA)
Sharma, Anuj& Manolakos, Elias S.. 2015. Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures. BioMed Research International،Vol. 2015, no. 2015, pp.1-13.
https://search.emarefa.net/detail/BIM-1055929
Modern Language Association (MLA)
Sharma, Anuj& Manolakos, Elias S.. Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures. BioMed Research International No. 2015 (2015), pp.1-13.
https://search.emarefa.net/detail/BIM-1055929
American Medical Association (AMA)
Sharma, Anuj& Manolakos, Elias S.. Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures. BioMed Research International. 2015. Vol. 2015, no. 2015, pp.1-13.
https://search.emarefa.net/detail/BIM-1055929
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1055929