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J Theor Biol. 2014 Apr 21;347:109-17. doi: 10.1016/j.jtbi.2014.01.001. Epub 2014 Jan 10.

A novel descriptor of protein sequences and its application.

Author information

  • 1College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China. Electronic address: yaoyuhua2288@163.com.
  • 2College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China.
  • 3College of Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China.

Abstract

In this paper, a dynamic 3-D graphical representation of protein sequences is introduced based on three physical-chemical properties of amino acids. The coordinates of the graph have direct biological significance, which could reflect the innate structure of the proteins. The information of principal moments of inertia and range of axis coordinate are extracted as a novel mixed descriptor and proposed for the comparison of protein primary sequences. Meanwhile, the Euclidean distance of the normalized descriptor vectors which avoid the influence of the difference in length of protein sequences under consideration is employed as a quantitative measurement of the similarity of proteins. Finally, we take the nine ND5 (NADH dehydrogenase subunit 5) proteins for example and illustrate the effectiveness of our approach.

Copyright © 2014 Elsevier Ltd. All rights reserved.

KEYWORDS:

Graphical representation; Protein descriptor; Similarities/dissimilarities

PMID:
24412564
[PubMed - indexed for MEDLINE]
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