This article has been accepted for inclusion in a future issue of this journal. Content is final as presented, with the exception of pagination. IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION 1 An Immune Algorithm for Protein Structure Prediction on Lattic

Abstract—We present an immune algorithm (IA) inspired by the clonal selection principle, which has been designed for the protein structure prediction problem (PSP). The proposed IA employs two special mutation operators, hypermutation and hypermacromuta-tion to allow effective searching, and an aging mechanism which is a new immune inspired operator that is devised to enforce diver-sity in the population during evolution. When cast as an optimization problem, the PSP can be seen as discovering a protein conformation with minimal energy. The pro-posed IA was tested on well-known PSP lattice models, the HP model in two-dimensional and three-dimensional square lattices’, and the functional model protein, which is a more realistic biolog-ical model. Our experimental results demonstrate that the proposed IA is very competitive with the existing state-of-art algorithms for the PSP on lattice models. Index Terms—Aging operator, clonal selection algorithms, func-tional model proteins, hypermacromutation operator, hypermuta-tion operator, immune algorithms (IAs), protein structure predic-tion problem, two-dimensional HP model, three-dimensional HP model. I