Non-Isomorphic Coding in Lattice Model and its Impact for Protein Folding Prediction Using Genetic Algorithm

Author

Hoque, Md Tamjidul ; Chetty, Madhu ; Dooley, Laurence S.

Author_Institution

Gippsland Sch. of Inf. Technol., Monash Univ., Clayton, Vic.

fYear

2006

fDate

28-29 Sept. 2006

Firstpage

1

Lastpage

8

Abstract

Traditional encodings for hydrophobic(H)-hydrophilic(P) model or HP lattice models is isomorphic, which adds unwanted variations for the same solution, thereby slowing convergence. In this paper a novel non-isomorphic encoding scheme is presented for HP lattice model, which constrains the search space. In addition, similarity comparisons are made easier and more consistent and it will be shown that non-deterministic search approach such as genetic algorithm (GA) converges faster when non-isomorphic encoding is employed

Keywords

biology computing; encoding; genetic algorithms; lattice theory; proteins; genetic algorithm; hydrophobic-hydrophilic lattice model; nonisomorphic coding; protein folding prediction; search space; Amino acids; Bonding; Encoding; Genetic algorithms; Information technology; Lattices; Predictive models; Proteins; Solid modeling; Surface acoustic waves;

fLanguage

English

Publisher

ieee

Conference_Titel

Computational Intelligence and Bioinformatics and Computational Biology, 2006. CIBCB '06. 2006 IEEE Symposium on

Conference_Location

Toronto, Ont.

Print_ISBN

1-4244-0623-4

Electronic_ISBN

1-4244-0624-2

Type

conf

DOI

10.1109/CIBCB.2006.331014

Filename

4133156