Analysis Of An Immune Algorithm For Protein Structure Prediction

The aim of a protein folding simulation is to determine the native state of a protein from its amino acid sequence. In this paper we describe the development and application of an Immune Algorithm (IA) to find the lowest energy conformations for the 2D (square) HP lattice bead protein model. Here we intro-duce a modified chain growth constructor to produce the initial population, where intermediate infeasible structures are recorded, thereby reducing the risk of attempting to perform wasteful point mutations during the mutation phase. We also investigate various approaches for population diversity tracking, ultimately allowing a greater understanding of the progress of the optimization.