On discrete models and immunological algorithms for protein structure prediction

Authors:
Vincenzo Cutello;Giuseppe Morelli;Giuseppe Nicosia;Mario Pavone;Giuseppe Scollo
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;Department of Mathematics and Computer Science, University of Catania, Catania, Italy
Venue:
Natural Computing: an international journal
Year:
2011

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Abstract

Discrete models for protein structure prediction embed the protein amino acid sequence into a discrete spatial structure, usually a lattice, where an optimal tertiary structure is predicted on the basis of simple assumptions relating to the hydrophobic---hydrophilic character of amino acids in the sequence and to relevant interactions for free energy minimization. While the prediction problem is known to be NP complete even in the simple setting of Dill's model with a 2D-lattice, a variety of bio-inspired algorithms for this problem have been proposed in the literature. Immunological algorithms are inspired by the kind of optimization that immune systems perform when identifying and promoting the replication of the most effective antibodies against given antigens. A quick, state-of-the-art survey of discrete models and immunological algorithms for protein structure prediction is presented in this paper, and the main design and performance features of an immunological algorithm for this problem are illustrated in a tutorial fashion.