A New Lamarckian Genetic Algorithm for Flexible Ligand-Receptor Docking
A New Lamarckian Genetic Algorithm for Flexible Ligand-Receptor Docking
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DOI：
10.1002/jcc.21478
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发表时间：
2010-07-15
影响因子：
3
通讯作者：
Neumann, Dirk
中科院分区：
文献类型：
--
作者：
Fuhrmann, Jan;Rurainski, Alexander;Neumann, Dirk
我们提出了一个拉马克遗传算法（LGA）的灵活的配体-受体对接，它允许处理大量的自由度的变体。我们的混合方法结合了一个多demeLGA与最近发表的基于梯度的方法，局部优化的分子复合物。我们比较了我们的新的混合方法的性能，两个非基于梯度的搜索算法的Astex多样的灵活的配体-受体时钟。我们的研究结果表明，新的方法是明显优于其他LGA采用随机优化方法上级。新的算法具有更短的运行时间，并给出了更好的结果，特别是随着配体的复杂性增加。因此，它可以用于以高效率对接具有许多可旋转键的配体。(c)2010 Wiley Periodicals，Inc.计算化学杂志31：1911- 1918，2010
We present a Lamarckian genetic algorithm (LGA) variant for flexible ligand-receptor docking which allows to handle a large number of degrees of freedom. Our hybrid method combines a multi-deme LGA with a recently published gradient-based method for local optimization of molecular complexes. We compared the performance of our new hybrid method to two non gradient-based search heuristics on the Astex diverse set for flexible ligand-receptor clocking. Our results show that the novel approach is clearly superior to other LGAs employing a stochastic optimization method. The new algorithm features a shorter run time and gives substantially better results, especially with increasing complexity of the ligands. Thus, it may be used to dock ligands with many rotatable bonds with high efficiency. (c) 2010 Wiley Periodicals, Inc. J Comput Chem 31: 1911-1918,2010