Protein Folding Simulation Based on Improved Simulated Annealing Algorithm

Jing Fa Liu; Zi Ling Zhou; Ze Xu Gao; Guo Jian Zhang

doi:10.4028/www.scientific.net/AMR.424-425.246

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HomeAdvanced Materials ResearchAdvanced Materials Research Vols. 424-425Protein Folding Simulation Based on Improved...

Protein Folding Simulation Based on Improved Simulated Annealing Algorithm

Abstract:

Protein folding problem is one of the most important problems in bioinformatics. By combining simulated annealing method with pull moves which is a local move set and conformation update mechanism, we put forward an improved simulated annealing (ISA) algorithm for the two-dimensional hydrophobic- polar (2D HP) protein folding problem. Numerical results show that the ISA algorithm can find the known lowest-energy ground state more rapidly and efficiently than the genetic algorithm (GA) for the several given HP sequences. For the sequence with length 20, we obtain the lower-energy conformation than GA. The performance of the algorithm show ISA is an effective method for protein folding simulation

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Periodical:

Advanced Materials Research (Volumes 424-425)

Pages:

246-249

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https://doi.org/10.4028/www.scientific.net/AMR.424-425.246

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Online since:

January 2012

Authors:

Jing Fa Liu, Zi Ling Zhou, Ze Xu Gao, Guo Jian Zhang

Keywords:

Lattice Model, Protein Folding, Pull Moves, Simulated Annealing Algorithm

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