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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