Title :
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
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;
Journal_Title :
Computational Biology and Bioinformatics, IEEE/ACM Transactions on
DOI :
10.1109/TCBB.2013.125
