Sulea Traian, Purisima Enrico O
Biotechnology Research Institute, National Research Council, Ottawa, ON, Canada.
Methods Mol Biol. 2012;819:295-303. doi: 10.1007/978-1-61779-465-0_19.
The solvated interaction energy (SIE) is an end-point, physics-based scoring function for predicting ligand-binding affinities. It supplements the force-field interaction energy with the desolvation cost of binding. Parameters such as the solute dielectric constant, Born radii, a cavity term and an overall scaling coefficient and additive constant have been previously calibrated against a training set of 99 protein-ligand complexes. We describe the application of the method to estimating binding free energies from molecular dynamics trajectories of protein-ligand binding complexes.
溶剂化相互作用能（SIE）是一种基于物理学的终点评分函数，用于预测配体结合亲和力。它通过结合的去溶剂化成本来补充力场相互作用能。诸如溶质介电常数、玻恩半径、空腔项、整体缩放系数和加性常数等参数，先前已针对99个蛋白质-配体复合物的训练集进行了校准。我们描述了该方法在根据蛋白质-配体结合复合物的分子动力学轨迹估算结合自由能方面的应用。
