力场(虚构)
计算机科学
计算科学
分子动力学
背景(考古学)
定制
图形处理单元
吞吐量
领域(数学)
蒙特卡罗方法
统计物理学
计算化学
物理
并行计算
化学
人工智能
古生物学
电信
统计
数学
政治学
纯数学
法学
无线
生物
作者
Lauren Nelson,Sofia Bariami,Chris Ringrose,Joshua T. Horton,Vadiraj Kurdekar,Antonia S. J. S. Mey,Julien Michel,D. J. A. Cole
标识
DOI:10.1021/acs.jcim.1c00328
摘要
The quantum mechanical bespoke (QUBE) force-field approach has been developed to facilitate the automated derivation of potential energy function parameters for modeling protein-ligand binding. To date, the approach has been validated in the context of Monte Carlo simulations of protein-ligand complexes. We describe here the implementation of the QUBE force field in the alchemical free-energy calculation molecular dynamics simulation package SOMD. The implementation is validated by demonstrating the reproducibility of absolute hydration free energies computed with the QUBE force field across the SOMD and GROMACS software packages. We further demonstrate, by way of a case study involving two series of non-nucleoside inhibitors of HIV-1 reverse transcriptase, that the availability of QUBE in a modern simulation package that makes efficient use of graphics processing unit acceleration will facilitate high-throughput alchemical free-energy calculations.
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