Data and code for "Dedu-Honghua-7-Wei San alleviates CCl4-induced hepatic fibrosis in mice: integrated network pharmacology, molecular simulation, and experimental validation"

Files are in XLSX, CSV, TSV, TXT, CYS (Cytoscape) and RData (R) formats.(2) 02_molecular_docking.zip (0.8 MB): one folder per protein-ligand complex (AKT1, EGFR and HIF-1alpha with luteolin and quercetin): receptor structures (PDB and PDBQT), ligand PDBQT files, AutoDock Vina 1.2.5 configuration files (grid centre and size), output poses (PDBQT, nine modes) and log files. The top-ranked pose of each output file is the pose reported in the manuscript.(3) 03_molecular_dynamics.zip (32.4 MB): one folder per complex from the 100 ns GROMACS 2022.2 simulations: md.log (complete parameter listing), md.tpr (run input including the topology), index.ndx, the analysis outputs RMSD, radius of gyration, SASA, hydrogen bonds and RMSF (XVG, GROMACS text format), and the MM/PBSA per-frame and per-residue outputs (DAT, plain text).

Standalone mdout.mdp files, ligand topology and starting structures, and final-frame GRO files are included where available. A standalone mdout.mdp file is not included for EGFR-luteolin; its run parameters are available in md.log and md.tpr. The final-frame GRO file is not included for HIF-1alpha-luteolin.

Trajectory files are available from the corresponding author on request.(4) 04_animal_data.zip (16 KB): body weight of every mouse (six groups x six mice, weeks 0 to 9; XLSX, one row per mouse, columns = weeks, unit g) and the histopathological injury score of every mouse (0 to 6 scale; XLSX), together with the R scripts and outputs of the repeated-measures ANOVA and Kruskal-Wallis/Dunn analyses.(5) 05_western_blot_raw_images.zip (25.1 MB): 27 uncropped membrane scans (TIF) for RAGE, HIF-1alpha and GAPDH, three membranes each, with the white-light molecular-weight marker image, the chemiluminescence image and their overlay.

File names follow the pattern protein_membraneN_imagetype.tif.