Molecular dynamics of the ERα ligand-binding domain with antidepressants, estradiol, PaPE-1 and a decoy: trajectories and inputs

Abstract

All-atom molecular dynamics of the human estrogen receptor alpha (ERα) ligand-binding domain bound to the SRC2 coactivator peptide (PDB 5WGD, wild type) with 17β-estradiol, PaPE-1, imipramine, (S)-ketamine, (2R,6R)-hydroxynorketamine, (R)-fluoxetine, (S)-fluoxetine, a DUD-E property-matched decoy, and the apo receptor. Each of the 9 systems was simulated in 3 independent replicas of 100 ns (ff14SB/GAFF2/TIP3P, 0.15 M NaCl, 310 K, GROMACS 2026, 4 fs with hydrogen mass repartitioning). Each replica provides the processed complex-only trajectory (10 ps per frame, molecules made whole and fitted on the pocket Cα atoms), the matching structure file, the run input (tpr) and energy file, and the GROMACS topology, coordinates and index of the starting system. Analysis code, small processed data and figures: https://github.com/masoudrezaei082-afk/eralpha-antidepressant-md.

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