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Journal of Information Science and Engineering, Vol.19 No.6, pp.943-952 (November 2003)


Finding Regularity in Various Types
of Secondary Protein Structures

Yen-Wei chu and Jinn-Moon Yang*
1Department of Computer and Information Science
*Department of Biological Science and Technology & Institute of Bioinformatics
National Chiao Tung University
Hsinchu, 300 Taiwan
E-mail: ywchu@cis.nctu.edu.tw
E-mail: moon@cc.nctu.edu.tw

Protein function is structurally determined, but analyzing the structure of a protein is both difficult and time-consuming. The authors look at the natural instincts of protein secondary structures, which used to be analyzed in terms of their statistical relationship with a single amino acid. Several schemas are offered for identifying regular patterns among various types of secondary protein structures. The schemas employ genetic algorithms based on a steady-state strategy. Two disjunctive data sets were used to verify fitness. The paper concludes with some illustrations of significant schemas produced as part of this study, with brief explanations of their significance.

Keywords: secondary protein structure, schema, steady-state genetic algorithm, rule extraction, sequence alignment, substitution matrix, voting mechanism, sequential pattern

Full Text () Retrieve PDF document (200311_03.pdf)

Received November 1, 2002; accepted June 5, 2003.
Communicated by Wen-Lian Hsu.