Power transformations improve interpolation of grids for molecular mechanics interaction energies,Journal of Computational Chemistry

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Power transformations improve interpolation of grids for molecular mechanics interaction energies
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2018-02-18 , DOI: 10.1002/jcc.25180
David D L Minh ₁

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A common strategy for speeding up molecular docking calculations is to precompute nonbonded interaction energies between a receptor molecule and a set of three‐dimensional grids. The grids are then interpolated to compute energies for ligand atoms in many different binding poses. Here, I evaluate a smoothing strategy of taking a power transformation of grid point energies and inverse transformation of the result from trilinear interpolation. For molecular docking poses from 85 protein‐ligand complexes, this smoothing procedure leads to significant accuracy improvements, including an approximately twofold reduction in the root mean square error at a grid spacing of 0.4 Å and retaining the ability to rank docking poses even at a grid spacing of 0.7 Å. © 2018 Wiley Periodicals, Inc.

中文翻译：

幂变换改进了分子力学相互作用能网格的插值

加速分子对接计算的常见策略是预先计算受体分子和一组三维网格之间的非键相互作用能量。然后对网格进行插值以计算配体原子在许多不同结合姿势下的能量。在这里，我评估了一种平滑策略，即对网格点能量进行幂变换并对三线性插值结果进行逆变换。对于 85 个蛋白质-配体复合物的分子对接姿势，这种平滑过程可显着提高准确性，包括在 0.4 Å 网格间距下均方根误差大约减少两倍，并且即使在网格上也保留对对接姿势进行排名的能力间距为 0.7 Å。© 2018 Wiley 期刊公司。

更新日期：2018-02-18

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