Novel local improvement techniques in clustered memetic algorithm for protein structure prediction

Evolutionary algorithms (EAs) often fail to find the global optimum due to genetic drift. As the protein structure prediction problem is multimodal having several global optima, EAs empowered with combined application of local and global search e.g., memetic algorithms, can be more effective. This paper introduces two novel local improvement techniques for the clustered memetic algorithm to incorporate both problem specific and search-space specific knowledge to find one of the optimum structures of a hydrophobic-polar protein sequence on lattice models. Experimental results show the superiority of the proposed techniques against existing EAs on benchmark sequences. © 2011 IEEE.