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.