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Effect of ligand torsion number on the AutoDock mediated prediction of protein-ligand binding affinity

机译：配体扭转数对蛋白质 - 配体结合亲和力的自动沸腾预测的影响

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摘要

Molecular docking simulation is a useful tool in the prediction of protein-ligand binding affinity on a large scale and has great potential in various application fields such as virtual screening of potential drug molecules. However, the reliability of molecular docking is still weak in the estimation of ligand-binding free energy, which limits the applicability of molecular docking simulation. Ligand torsion number is related to the flexibility of ligand and generally incorporated as a crucial variable in the thermodynamic function of binding free energy. In this study, we investigated how the ligand torsion number has influence on the binding affinity prediction of AutoDock, a popular molecular docking simulation tool. The pK(d) values of various protein-ligands were estimated by using the binding free energy function of AutoDock and compared with their experimental pK(d) values. The torsion number dependent comparison showed that the predicted binding affinities were mostly underestimated in the complexes of higher torsion numbers, whereas the underestimated and overestimated cases were relatively balanced at relatively lower torsion numbers. A new weight factor for torsion-free energy term of binding energy function was determined and introduced to make correction to the underestimation of binding affinity of ligands with high torsion numbers. It is expected that the torsion number dependent deviation pattern of AutoDock and its correction strategy are useful in the large-scale validation of protein-ligand binding affinity. (C) 2019 The Korean Society of Industrial and Engineering Chemistry. Published by Elsevier B.V. All rights reserved.
机译：分子对接模拟是在大规模上预测蛋白质 - 配体结合亲和力的有用工具，并且在各种应用领域具有很大的潜力，例如潜在药物分子的虚拟筛选。然而，分子对接的可靠性在估计配体结合能量的估计中仍然弱，这限制了分子对接模拟的适用性。配体扭转数与配体的柔韧性有关，并且通常在结合自由能的热力学函数中作为关键变量掺入。在这项研究中，我们研究了配体扭转数对自动分子对接模拟工具的自动频道的结合亲和力预测的影响。通过使用Autodock的结合可自由能功能来估计各种蛋白质 - 配体的PK（D）值，并与其实验PK（D）值进行比较。扭转数依赖性比较表明，预测的结合亲和力大多低估在较高扭转数的络合物中，而低估和高估的病例在相对较低的扭转数中相对平衡。确定并引入结合能量功能的无扭转能量术语的新重量因子，以校正以低估配体具有高扭转数的结合亲和力。预计Autodock的扭转数依赖性偏差模式及其校正策略可用于蛋白质 - 配体结合亲和力的大规模验证。 （c）2019年韩国工程化学学会。 elsevier b.v出版。保留所有权利。

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