According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the unbound ligand ensemble and a rigid receptor. Here, we use the fast Fourier transform (FFT) to efficiently evaluate BPMFs by calculating interaction energies when rigid ligand configurations from the unbound ensemble are discretely translated across rigid receptor conformations. Results for standard binding free energies between T4 lysozyme and 141 small organic molecules are in good agreement with previous alchemical calculations based on (1) a flexible complex ( R≈0.9 for 24 systems) and (2) flexible ligand with multiple rigid receptor configurations ( R≈0.8 for 141 systems). While the FFT is routinely used for molecular docking, to our knowledge this is the first time that the algorithm has been used for rigorous binding free energy calculations. © 2017 Wiley Periodicals, Inc.

中文翻译：

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在结合自由能计算中使用快速傅立叶变换

根据隐式配体理论，标准结合自由能是平均力结合势 (BPMF) 的指数平均值，即未结合配体整体与刚性受体之间相互作用能的指数平均值。在这里，我们使用快速傅立叶变换 (FFT) 通过计算相互作用能来有效评估 BPMF，当来自未结合集合的刚性配体配置在刚性受体构象中离散转换时。T4 溶菌酶与 141 种有机小分子之间的标准结合自由能结果与之前基于 (1) 柔性复合物（24 个系统的 R≈0.9）和 (2) 具有多个刚性受体构型的柔性配体的炼金术计算非常一致对于 141 个系统，R≈0.8）。虽然 FFT 通常用于分子对接，据我们所知，这是该算法首次用于严格的结合自由能计算。© 2017 威利期刊公司。