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A Multi-core Tool for Searching Protein Structural Similarities

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International Journal of Computer Applications
© 2012 by IJCA Journal
Volume 50 - Number 12
Year of Publication: 2012
Authors:
Ahmed Salah
Kenlili
Tarek F. Gharib
Abdul Fattah Mashat
10.5120/7825-1015

Ahmed Salah, Kenlili, Tarek F Gharib and Abdul Fattah Mashat. Article: A Multi-core Tool for Searching Protein Structural Similarities. International Journal of Computer Applications 50(12):34-36, July 2012. Full text available. BibTeX

@article{key:article,
	author = {Ahmed Salah and Kenlili and Tarek F. Gharib and Abdul Fattah Mashat},
	title = {Article: A Multi-core Tool for Searching Protein Structural Similarities},
	journal = {International Journal of Computer Applications},
	year = {2012},
	volume = {50},
	number = {12},
	pages = {34-36},
	month = {July},
	note = {Full text available}
}

Abstract

The analysis of protein structural similarities plays an important role in different biological fields. These fields vary from the process of developing new drugs to detecting the evolutionrelationships. As the number of protein structures grows rapidly there is an increasing demand for improving the speed of the computational tools that handles proteome. The wide prevalence of multi cores computers and its low price can be employed to speed up the existing tools used for searching protein structural similarities. In this report, we present a modified version of a PSISA tool, which efficiently used to find the structural similarities between different proteins and maintains the load balance between cores. Using an Intel 8 cores computer and the structural classification of proteins (SCOP) dataset, the experiments show an average speed up 1. 8 using 8 cores without affecting the memory usage or the accuracy of the tool.

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