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

Brazilian Computer Society. Journal

rio Lopes¹  Cé²  Heitor Silvé³  sar Manuel Vargas Bení⁴  tez⁵ 

[1] , Curitiba, Brazil;Laboratógica Federal do Paranário de Bioinformática, CPGEI, Universidade Tecnoló

关键词: Genetic algorithm;    Bioinformatics;    Protein folding;    3D-HP-SC;   

DOI  :  10.1007/s13173-010-0002-6

学科分类：农业科学（综合）

来源: Springer U K

【 摘 要 】

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.

【 授权许可】

CC BY