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Cluster protein structures using recurrence quantification analysis on coordinates of alpha-carbon atoms of proteins

Zhou, Yu, Yu, Zu-Guo, & Anh, Vo V. (2007) Cluster protein structures using recurrence quantification analysis on coordinates of alpha-carbon atoms of proteins. Physics Letters. Section A: General, Atomic and Solid State Physics, 368(3/4), pp. 314-319.

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Abstract

The 3-dimensional coordinates of alpha-carbon atoms of proteins are used to distinguish the protein structural classes based on recurrence quantification analysis (RQA). We consider two independent variables from RQA of coordinates of alpha-carbon atoms, %determ1 and %determ2, which were defined by Webber et al. [C.L. Webber Jr., A. Giuliani, J.P. Zbilut, A. Colosimo, Proteins Struct. Funct. Genet. 44 (2001) 292]. The variable %determ2 is used to define two new variables, %determ21 and %determ22. Then three variables %determ1, %determ21 and %determ22 are used to construct a 3-dimensional variable space. Each protein is represented by a point in this variable space. The points corresponding to proteins from the α, β, α+β and α/β structural classes position into different areas in this variable space. In order to give a quantitative assessment of our clustering on the selected proteins, Fisher's discriminant algorithm is used. Numerical results indicate that the discriminant accuracies are very high and satisfactory.

Impact and interest:

7 citations in Scopus
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7 citations in Web of Science®

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ID Code: 14802
Item Type: Journal Article
DOI: 10.1016/j.physleta.2007.04.012
ISSN: 0375-9601
Subjects: Australian and New Zealand Standard Research Classification > MATHEMATICAL SCIENCES (010000) > APPLIED MATHEMATICS (010200) > Biological Mathematics (010202)
Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > BIOCHEMISTRY AND CELL BIOLOGY (060100) > Protein Trafficking (060108)
Australian and New Zealand Standard Research Classification > MATHEMATICAL SCIENCES (010000) > PURE MATHEMATICS (010100) > Ordinary Differential Equations Difference Equations and Dynamical Systems (010109)
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Copyright Owner: Copyright 2007 Elsevier
Copyright Statement: Reproduced in accordance with the copyright policy of the publisher.
Deposited On: 12 Sep 2008
Last Modified: 29 Feb 2012 23:40

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