Immune Algorithms with Aging Operators for the String Folding Problem and the Protein Folding Problem

• Published in: Evolutionary Computation in Combinatorial Optimization pp. 80 - 90
• Main Authors: Cutello, V., Morelli, G., Nicosia, G., Pavone, M.
• Format: Book Chapter Conference Proceeding
• Language: English
• Published: Berlin, Heidelberg Springer Berlin Heidelberg 2005; Springer
• Series: Lecture Notes in Computer Science
• Subjects: aging operator; Applied sciences; Clonal selection algorithms; Computer science; control theory; systems; Exact sciences and technology; Flows in networks. Combinatorial problems; functional model proteins; HP model; Logical, boolean and switching functions; memory B cells; Operational research and scientific management; Operational research. Management science; protein structure prediction; Theoretical computing; Immune algorithm; Landscape; Genetic algorithm; Character string; Evolutionary algorithm; Longevity; Molecular biology; Combinatorial optimization; Modeling; Protein structure; Protein; Lattice
• ISBN: 9783540253372; 3540253378
• ISSN: 0302-9743; 1611-3349
• DOI: 10.1007/978-3-540-31996-2_8

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.