Dataset for MD and MM/GBSA-Based Evalulation of Ternary Complexes Induced by Proteolysis Targeting Chimeras (PROTACs) for Targeted Protein Degradation

This is the dataset for all input files, output files/results, and submit script or its templates for running the MD and MMGBSA calculations in the paper. Four compressed archives represent the 4 systems we ran our simulations on. The general workflow for all systems follow the sequence of, after starting pose generated by protein docking, the starting frame for MD and its parameter file is generated in the Tleap folder; the MD trajectories are found in the PMEMD folders; and the energy calculations are found in the MMGBSA folders.本数据集涵盖本论文中运行分子动力学（MD, Molecular Dynamics）与分子力学/广义玻恩表面积（MMGBSA, Molecular Mechanics/Generalized Born Surface Area）计算所需的全部输入文件、输出文件及计算结果，以及提交脚本或其模板。四个压缩包对应本研究开展模拟实验所用的4套体系。所有体系的通用计算流程遵循如下顺序：首先通过蛋白质对接（protein docking）生成初始构象，随后在Tleap文件夹中生成MD模拟的初始帧及其参数文件；MD模拟轨迹存储于PMEMD文件夹中；能量计算结果则存放于MMGBSA文件夹中。