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A New Approach for Flexible Molecular Docking Based on Swarm Intelligence

机译：基于群体智能的柔性分子对接新方法

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摘要

Molecular docking methods play an important role in the field of computer-aided drug design. In the work, on the basis of the molecular docking program AutoDock, we present QLDock as a tool for flexible molecular docking. For the energy evaluation, the algorithm uses the binding free energy function that is provided by the AutoDock 4.2 tool. The new search algorithm combines the features of a quantum-behaved particle swarm optimization (QPSO) algorithm and local search method of Solis and Wets for solving the highly flexible protein-ligand docking problem. We compute the interaction of 23 protein-ligand complexes and compare the results with those of the QDock and AutoDock programs. The experimental results show that our approach leads to substantially lower docking energy and higher docking precision in comparison to Lamarckian genetic algorithm and QPSO algorithm alone. QPSO-ls algorithm was able to identify the correct binding mode of 74% of the complexes. In comparison, the accuracy of QPSO and LGA is 52% and 61%, respectively. This difference in performance rises with increasing complexity of the ligand. Thus, the novel algorithm QPSO-ls may be used to dock ligand with many rotatable bonds with high accuracy.
机译：分子对接方法在计算机辅助药物设计领域中起着重要作用。在工作中，基于分子对接程序AutoDock，我们介绍了QLDock作为灵活的分子对接工具。对于能量评估，该算法使用由AutoDock 4.2工具提供的无约束力自由能函数。新的搜索算法结合了量子行为粒子群优化（QPSO）算法的特征以及Solis和Wets的局部搜索方法，以解决高度灵活的蛋白质-配体对接问题。我们计算了23种蛋白质-配体复合物的相互作用，并将结果与​​QDock和AutoDock程序进行了比较。实验结果表明，与单独的Lamarckian遗传算法和QPSO算法相比，我们的方法可大大降低对接能量并提高对接精度。 QPSO-ls算法能够识别74％的复合物的正确结合模式。相比之下，QPSO和LGA的准确性分别为52％和61％。这种性能差异随着配体复杂性的增加而增加。因此，新颖的算法QPSO-1s可以用于以高精度对接具有许多可旋转键的配体。

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  • 来源
    《Mathematical Problems in Engineering》 |2015年第7期|540186.1-540186.10|共10页
  • 作者

    Fu Yi; Wu Xiaojun; Chen Zhiguo; Sun Jun; Zhao Ji; Xu Wenbo;

  • 作者单位

    Jiangnan Univ, Sch Internet Things Engn, Wuxi 214122, Jiangsu, Peoples R China.;

    Jiangnan Univ, Sch Internet Things Engn, Wuxi 214122, Jiangsu, Peoples R China.;

    Jiangnan Univ, Sch Internet Things Engn, Wuxi 214122, Jiangsu, Peoples R China.;

    Jiangnan Univ, Sch Internet Things Engn, Wuxi 214122, Jiangsu, Peoples R China.;

    Wuxi City Coll Vocat Technol, Dept Elect & Informat Engn, Wuxi 214153, Jiangsu, Peoples R China.;

    Jiangnan Univ, Sch Internet Things Engn, Wuxi 214122, Jiangsu, Peoples R China.;

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