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BioMed Research International
Volume 2015, Article ID 563674, 13 pages
Research Article

Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures

Department of Informatics and Telecommunications, University of Athens, Athens, Greece

Received 24 July 2015; Revised 4 October 2015; Accepted 5 October 2015

Academic Editor: Yudong Cai

Copyright © 2015 Anuj Sharma and Elias S. Manolakos. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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 high -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.