Protein structure prediction with the 3D-HP side-chain model using a master–slave parallel genetic algorithm

César Manuel Vargas Benítez,Heitor Silvério Lopes

doi:10.1007/s13173-010-0002-6

Abstract

Abstract This work presents a master-slave parallel genetic algorithm for the protein folding problem, using the 3D-HP side-chain model (3D-HP-SC). This model is sparsely studied in the literature, although more expressive than other lattice models. The fitness function proposed includes information not only about the free-energy of the conformation, but also compactness of the side-chains. Since there is no benchmark available to date for this model, a set of 15 sequences was used, based on a simpler model. Results show that the parallel GA achieved a good level of efficiency and obtained biologically coherent results, suggesting the adequacy of the methodology. Future work will include new biologically-inspired genetic operators and more experiments to create new benchmarks.

Highlights

IntroductionProteins are polymers composed by a chain of amino acids ( called residues) that are linked together by means of peptide bonds
Proteins are polymers composed by a chain of amino acids that are linked together by means of peptide bonds
This paper is an extended version of a paper that appeared at ENIA 2009 (The Brazilian Meeting on Artificial Intelligence)

Summary

Introduction

Proteins are polymers composed by a chain of amino acids ( called residues) that are linked together by means of peptide bonds. The protein folds into a unique 3dimensional structure. The specific shape to which the protein naturally folds is known as its native conformation. The specific biological function of a protein depends on its 3dimensional shape, which in turn, is a function of its primary structure (its linear sequence of amino acids). Failure to fold into the intended 3-dimensional shape usually leads to proteins with different properties that become inactive. In the worst case, such misfolded (incorrectly folded) proteins can be harmful to the organism. Several diseases such as Alzheimer’s disease, cystic fibrosis, and some types of cancer, are believed to result from the accumulation of misfolded proteins

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