Molecular Dynamics Dataset of Sequential Allosteric Locking of the Insect Ecdysone Receptor by Azadirachtin and Eugenol

This repository contains the complete computational dataset supporting the manuscript "Sequential Allosteric Locking of the Insect Ecdysone Receptor by Azadirachtin and Eugenol Reveals Phytochemical Synergy." The dataset has been organized to enable full reproducibility of the molecular docking, molecular dynamics simulations, and post-simulation analyses presented in the study. The repository includes simulation input files, molecular docking files, representative average structures, processed molecular dynamics trajectories, analysis scripts, raw analysis outputs, publication-quality figures, statistical reports, residue mapping tables, and supplementary LaTeX resources used during manuscript preparation. Repository Structure 01_simulation_inputs – GROMACS molecular dynamics parameter files (.mdp) and simulation topologies. 02_docking – Docking receptor/ligand structures, docking logs, GNINA outputs, and redocking scripts. 03_average_structures – Average structures generated from equilibrated MD trajectories. 04_trajectories – Processed production trajectories (.xtc) and corresponding topology (.tpr) files. 05_analysis_scripts – Python and shell scripts used for all trajectory analyses, including PCA, DCCM, MM/GBSA processing, hydrogen-bond analysis, residue interaction networks, pocket volume calculations, Boltzmann inversion, residence analysis, and reviewer-requested analyses. 06_analysis_data – Raw numerical outputs generated from all computational analyses. 07_figures – Publication-quality figures used in the manuscript and supplementary information. 08_latex_tables – LaTeX tables included in the manuscript. 09_statistical_reports – Statistical summaries and quality-control reports. 10_residue_mapping – Residue numbering correspondence tables. README.md – Repository overview and usage instructions. file_manifest.txt – Manifest listing all files included in the dataset. Software The simulations and analyses were performed primarily using: GROMACS Python GNINA AutoDock Vina CHARMM-GUI CHARMM36m force field MM/GBSA analysis tools Custom Python analysis scripts included in this repository Trajectory Archive Reconstruction To facilitate reliable upload and download, the trajectory archive was split into multiple parts. Reconstruct the archive using: cat 04_trajectories.tar.zst.part.* > 04_trajectories.tar.zst Extract using: tar --use-compress-program=zstd -xf 04_trajectories.tar.zst Reproducibility All scripts, processed trajectories, intermediate analysis files, statistical outputs, and publication figures necessary to reproduce the computational analyses are included. The repository is intended to provide a transparent and reproducible computational workflow accompanying the associated publication.