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Flexible protein-ligand docking using particle swarm optimization

机译：使用粒子群优化对接柔性蛋白质 - 配体对接

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Many protein-ligand docking problems attempt to predict the bound conformations of two interacting molecules. Consequently, the docking problem requires a powerful search technique to explore the translations, orientations, and each torsion until an ideal site has been found. Therefore, protein-ligand docking can be formulated as a parameter optimization problem. However, highly flexible ligands have a lot of torsions. Therefore, the optimization problem of highly flexible docking would become more difficult due to the increment of parameter number and interactions among these parameters. We proposed a novel method SODOCK based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems. PSO has significant effect on the optimization of parameters with strong interactions. A commonly used efficient local search is incorporated into SODOCK to improve the efficiency and robustness of PSO. SODOCK is efficient for both types of ligands with small and large numbers of torsions. It is shown by computer simulation that SODOCK performs well in obtaining accurate conformations, compared with some of state-of-the-art methods. Moreover, it is also shown that SODOCK is superior to AutoDock using the same energy function in AutoDock 3.05 in terms of convergence speed, robustness, and docking energy, especially for highly flexible docking problems.
机译：许多蛋白质 - 配体对接问题试图预测两个相互作用分子的结合构象。因此，对接问题需要强大的搜索技术来探索翻译，方向和每个扭转，直到找到理想站点。因此，可以将蛋白质 - 配体对接配制成参数优化问题。然而，高度柔性配体具有很多扭转。因此，由于这些参数之间的参数数量和交互增加，高度灵活的对接的优化问题将变得更加困难。我们提出了一种基于粒子群优化（PSO）的新型方法SOOPOOK，用于求解柔性蛋白质 - 配体对接问题。 PSO对具有强烈相互作用的参数的优化具有显着影响。常用的有效本地搜索被纳入灌溉中，以提高PSO的效率和稳健性。索罗对两种类型的配体有效，具有小而大量的扭转。与一些最先进的方法相比，通过计算机模拟显示索索尔在获得准确的构象时表现良好。此外，还示出了在收敛速度，鲁棒性和对接能量方面，使用相同的能量函数在Autodock 3.05中使用相同的能量功能，特别是对于高度灵活的对接问题。

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