Protein Structure Optimization with a "Lamarckian"´ Ant Colony Algorithm

Author

Oakley, Mark T. ; Richardson, E. Grace ; Carr, Harriet ; Johnston, Roy L.

Author_Institution

Sch. of Chem., Univ. of Birmingham, Birmingham, UK

Volume

10

Issue

6

fYear

2013

fDate

Nov.-Dec. 2013

Firstpage

1548

Lastpage

1552

Abstract

We describe the LamarckiAnt algorithm: a search algorithm that combines the features of a "Lamarckian" genetic algorithm and ant colony optimization. We have implemented this algorithm for the optimization of BLN model proteins, which have frustrated energy landscapes and represent a challenge for global optimization algorithms. We demonstrate that LamarckiAnt performs competitively with other state-of-the-art optimization algorithms.

Keywords

ant colony optimisation; biological techniques; biology computing; genetic algorithms; molecular biophysics; proteins; search problems; BLN model protein optimization; Lamarckian ant colony algorithm; Lamarckian genetic algorithm; ant colony optimization; frustrated energy landscapes; global optimization algorithms; protein structure optimization; search algorithm; Bioinformatics; Computational biology; Genetic algorithms; Minimization; Optimization; Proteins; Ant colony optimization; coarse-grained model proteins;

fLanguage

English

Journal_Title

Computational Biology and Bioinformatics, IEEE/ACM Transactions on

Publisher

ieee

ISSN

1545-5963

Type

jour

DOI

10.1109/TCBB.2013.125

Filename

6624115