求解蛋白质折叠问题的模拟退火算法

Simulated Annealing Algorithm for Protein Folding Problem

通过构造新的数学模型,把三维AB模型的蛋白质折叠问题由一个带约束的优化问题转化为无约束优化问题,然后提出一个模拟退火算法.对如何得到初始构形,提出了一个启发式策略.实算结果表明,本文算法效率较高,对四条氨基酸测试序列,本文算法得到的最低能量都要优于nPERM算法得到的结果.

By constructinga new mathematic model, the protein folding problem of three-dimensional AB model is converted from a nonlinear constraint-satisfied problem to an unconstrained optimization problem. A simulated annealing algorithm is proposed for solving this unconstrained optimization problem and an effective heuristic strategy is introduced for generating better initial configuration. The computational results show that our algorithm can outperform nPERM algorithm in terms of finding states with lower energy for the four benchmark sequences.