Immune algorithms with aging operators for the string folding problem and the protein folding problem

Authors:
V. Cutello;G. Morelli;G. Nicosia;M. Pavone
Affiliations:
Department of Mathematics and Computer Science, University of Catania, Catania, Italy;Department of Mathematics and Computer Science, University of Catania, Catania, Italy;Department of Mathematics and Computer Science, University of Catania, Catania, Italy;Department of Mathematics and Computer Science, University of Catania, Catania, Italy
Venue:
EvoCOP'05 Proceedings of the 5th European conference on Evolutionary Computation in Combinatorial Optimization
Year:
2005

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Abstract

We present an Immune Algorithm (IA) based on clonal selection principle and which uses memory B cells, to face the protein structure prediction problem (PSP) a particular example of the String Folding Problem in 2D and 3D lattice. Memory B cells with a longer life span are used to partition the funnel landscape of PSP, so to properly explore the search space. The designed IA shows its ability to tackle standard benchmarks instances substantially better than other IA’s. In particular, for the 3D HP model the IA allowed us to find energy minima not found by other evolutionary algorithms described in literature.