Using genetic algorithm to design protein sequence

• Published in: Applied mathematics and computation Vol. 200; no. 1; pp. 1 - 9
• Main Authors: Scott, Luis P.B., Chahine, Jorge, Ruggiero, José R.
• Format: Journal Article
• Language: English
• Published: New York, NY Elsevier Inc 15.06.2008; Elsevier
• Subjects: Bioinformatics; Calculus of variations and optimal control; Combinatorics; Combinatorics. Ordered structures; Designs and configurations; Exact sciences and technology; Genetic algorithms; Mathematical analysis; Mathematics; Numerical analysis; Numerical analysis. Scientific computation; Numerical methods in mathematical programming, optimization and calculus of variations; Optimization; Prediction; Protein structure; Sciences and techniques of general use; Protein structure; Bioinformatics; Optimization; Prediction; Genetic algorithms; Numerical analysis; Genetic algorithm; Applied mathematics; Optimization method; Mathematical programming
• ISSN: 0096-3003; 1873-5649
• DOI: 10.1016/j.amc.2007.09.033

In this work, genetic algorithms concepts along with a rotamer library for proteins side chains are used to optimize the tertiary structure of the hydrophobic core of Cytochrome b 562 starting from the known PDB structure of its backbone which is kept fixed while the side chains of the hydrophobic core are allowed to adopt the conformations present in the rotamer library. The atoms of the side chains forming the core interact via van der Waals energy. Besides the prediction of the native core structure, it is also suggested a set of different amino acid sequences for this core. Comparison between these new cores and the native are made in terms of their volumes, van der Waals energies values and the numbers of contacts made by the side chains forming the cores. This paper proves that genetic algorithms area efficient to design new sequence for the protein core.