Title :
An Immune Algorithm for Protein Structure Prediction on Lattice Models
Author :
Cutello, Vincenzo ; Nicosia, Giuseppe ; Pavone, Mario ; Timmis, Jonathan
Author_Institution :
Dept. of Math. & Comput. Sci., Catania Univ.
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 hypermacromutation to allow effective searching, and an aging mechanism which is a new immune inspired operator that is devised to enforce diversity 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 proposed 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 biological 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
Keywords :
artificial immune systems; biocomputing; proteins; clonal selection principle; hypermacromutation; hypermutation; immune algorithm; lattice models; protein structure prediction; Aging; Algorithm design and analysis; Biological system modeling; Evolution (biology); Genetic mutations; Immune system; Lattices; Predictive models; Proteins; Testing; Aging operator; clonal selection algorithms; functional model proteins; hypermacromutation operator; hypermutation operator; immune algorithms (IAs); protein structure prediction problem; three-dimensional HP model; two-dimensional HP model;
Journal_Title :
Evolutionary Computation, IEEE Transactions on
DOI :
10.1109/TEVC.2006.880328