Extremal Optimization for the Protein Structure Alignment

Author

Lu, Hengyun ; Yang, Genke ; Yeung, Lam Fat

Author_Institution

Dept. of Autom., Shanghai Jiao Tong Univ., Shanghai, China

fYear

2009

fDate

1-4 Nov. 2009

Firstpage

15

Lastpage

19

Abstract

This paper proposes a combinational optimization algorithm extremal optimization (EO) for protein structure alignment based on the contact map overlap (CMO) model. EO is a meta-heuristic algorithm, as genetic algorithm and simulated annealing, but with a local fitness introduced to guide the improvement of the optimization. By exploiting similarity matrix between two contact maps, the results demonstrate that our algorithm is significantly faster and gets better results for most of the test sets.

Keywords

biology computing; genetic algorithms; molecular biophysics; proteins; simulated annealing; combinational optimization algorithm extremal optimization; contact map overlap model; genetic algorithm; meta-heuristic algorithm; protein structure alignment; simulated annealing; Automation; Bioinformatics; Biomedical engineering; Genetic algorithms; Heuristic algorithms; Optimization methods; Prediction algorithms; Protein engineering; Simulated annealing; Testing; extremal optimization; protein alignment; the contact map overlap;

fLanguage

English

Publisher

ieee

Conference_Titel

Bioinformatics and Biomedicine, 2009. BIBM '09. IEEE International Conference on

Conference_Location

Washington, DC

Print_ISBN

978-0-7695-3885-3

Type

conf

DOI

10.1109/BIBM.2009.48

Filename

5341878