[1]刘燕茹,石继飞,罗利霞. 一种基于均匀设计原理的自适应克隆选择分子对接构像搜索策略[J].中国医学物理学杂志,2018,35(7):828-832.[doi:DOI:10.3969/j.issn.1005-202X.2018.07.017]
　LIU Yanru,SHI Jifei,LUO LixiaBaotou Medical College,et al. A molecular docking conformational search strategy of adaptive clonal selection algorithm based on principle of uniform design[J].Chinese Journal of Medical Physics,2018,35(7):828-832.[doi:DOI:10.3969/j.issn.1005-202X.2018.07.017]
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 一种基于均匀设计原理的自适应克隆选择分子对接构像搜索策略()
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《中国医学物理学杂志》[ISSN:1005-202X/CN:44-1351/R]

卷:
35卷
期数:
2018年第7期
页码:
828-832
栏目:
医学生物物理
出版日期:
2018-07-20

文章信息/Info

Title:
 A molecular docking conformational search strategy of adaptive clonal selection algorithm based on principle of uniform design
文章编号:
1005-202X（2018）07-0828-05
作者:
刘燕茹; 石继飞; 罗利霞
 包头医学院， 内蒙古 包头 014040
Author(s):
 LIU Yanru;  SHI Jifei;  LUO LixiaBaotou Medical College;  Baotou 014040;  China
 Baotou Medical College, Baotou 014040, China
关键词:
 ; 分子对接; 构象搜索策略; 均匀设计; 自适应; 克隆选择算法
Keywords:
 ; Keywords: molecular docking;  conformational search strategy;  uniform design;  adaptive;  clonal selection algorithm
分类号:
TP306.1；R35
DOI:
DOI:10.3969/j.issn.1005-202X.2018.07.017
文献标志码:
A
摘要:
 为提高分子对接精度与速度，设计且实现了基于均匀设计原理的自适应克隆选择自动分子对接搜索策略。该策略首先引入抗体浓度，用抗体浓度和最低结合自由能共同衡量抗体品质；并利用均匀设计原理设计了克隆选择算法各参数的组合式样；然后利用自适应的克隆增殖、自适应的变异以及自适应的重组算子替代了克隆选择、高频变异以及简单重组算子。为验证该对接方法的有效性，用此方法对布克海文蛋白质数据库中的6种蛋白质—配体复合物进行实验测试，并将实验结果与拉马克遗传算法、模拟退火算法、免疫遗传算法和简单克隆选择算法进行比较，实验表明该对接策略具有更快的收敛速度和更好的寻优能力。
Abstract:
 Abstract: A conformational search strategy of adaptively clonal selection algorithm based on the principle of uniform design principle is designed and realized in molecular docking for improving the accuracy and speed of molecular docking. Firstly, the antibody concentration is introduced into the strategy, and the antibody quality is evaluated by antibody concentration and minimum binding free energy. Then, the principle of uniform design is used to design the combination of various parameters for clonal selection algorithm. Finally, adaptive clonal selection, adaptive mutation, adaptive recombination are applied to replace clonal selection, mutation, recombination. For verifying the performance of the proposed algorithm, tests are conducted on 6 kinds of protein-ligands complex from Brookhaven PDB protein database, and the proposed algorithm is also compared with Lamarckian genetic algorithm, simulated annealing algorithm, immune genetic algorithm and clonal selection algorithm. The results show that the proposed algorithm is faster in convergence and has better searching ability.

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备注/Memo

备注/Memo:
 【收稿日期】2018-02-15
【基金项目】内蒙古自治区高等学校科学研究项目（NJZY14266）
【作者简介】刘燕茹，研究方向：最优化算法、生物信息学，E-mail: liumin_1009@126.com
更新日期/Last Update: 2018-07-24