A combination of numeric genetic algorithm and tabu search can be applied to molecular docking
A combination of numeric genetic algorithm and tabu search can be applied to molecular docking
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DOI：
10.1016/j.compbiolchem.2004.08.002
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发表时间：
2004-10-01
影响因子：
3.1
通讯作者：
Li, TH
中科院分区：
文献类型：
--
作者：
Cao, TC;Li, TH
将数值遗传算法（NGA）和禁忌搜索算法（TS）结合成一个工具（NGA-TS）。NGA-TS通过计算基于保留时间和洗涤条件之间的关系的模拟系统，可以提高搜索算法的效率，避免陷入局部最优。计算机辅助药物设计是近年来一个活跃的研究领域。我们的分子对接程序与NGA-TS作为一种搜索技术，可以在PC上运行。经验自由能值用于评分函数的能力。通过对β-胰蛋白酶/苯甲脒体系的计算，验证了程序的性能。此外，还研究了100个蛋白质-配体复合物的测试集。并与Autodock程序和ConsDock程序进行比较。建议的NGA-TS搜索方法似乎是更有效的计算复杂性（即更少的内存和时间消耗）比其他常规搜索技术。因此，它可以有效地应用于大型数据库的虚拟筛选。
We combined the numeric genetic algorithm (NGA) and tabu search algorithm (TS) into a single tool (NGA-TS). Through computing a simulated system based on the relationship between the retention times and washing conditions, the NGA-TS can enhance the efficiency of the search algorithm and avoid entrapment into local optima. Computer-aided drug design has been an active research field in recent years. Our molecular docking program with NGA-TS as a search technique can be run on a PC. Empirical free energy values are used in the capacity of the scoring function. The performance of the program was verified by computing the beta-trypsin/benzamidine system. In addition, a test set of 100 protein-ligands complexes was studied as well. The results were compared with those of Autodock program and ConsDock. The proposed NGA-TS search methodology appears to be more efficient in terms of computational complexity (i.e. less memory and time consuming) than other routine search techniques. Therefore, it could be effectively applied to virtual screening of large databases.