2026-10-14T12:24:18Z https://www.scidb.cn/oai

10.57760/sciencedb.013wh 2026-09-28T15:58:39Z

2026-09-28 Data and code for "Dedu-Honghua-7-Wei San alleviates CCl4-induced hepatic fibrosis in mice: integrated network pharmacology, molecular simulation, and experimental validation" doi:10.57760/sciencedb.013wh en This dataset contains the raw and processed data supporting the manuscript "Dedu-Honghua-7-Wei San alleviates CCl4-induced hepatic fibrosis in mice: integrated network pharmacology, molecular simulation, and experimental validation" (Brazilian Journal of Pharmaceutical Sciences, manuscript BJPS-2026-0505). The data were generated between 2025 and 2026 at Qingshuihe County Medical Group and Hohhot Hospital of Traditional Chinese and Mongolian Medicine, Hohhot, China. The dataset comprises five compressed folders (ZIP) and a README.md file.(1) 01_network_pharmacology.zip (10.8 MB): database exports of the constituents of the six botanical components of DDHH-7 from TCMSP (oral bioavailability ≥ 30%, drug-likeness ≥ 0.18) and BATMAN-TCM 2.0 (score > 0.84), SwissTargetPrediction results for Scabiosa comosa constituents, OMIM and GeneCards (relevance score > 20) exports for hepatic fibrosis (all accessed in April 2025), the compound, target and disease-target tables (213 compounds, 247 herb-compound records, 1,681 targets, 531 disease targets, 190 overlapping targets), the STRING interaction table (Homo sapiens, minimum score 0.4), two Cytoscape 3.8.2 session files (.cys) with topology tables and the cytoHubba MCC ranking, and the clusterProfiler GO and KEGG enrichment results (R data objects .RData and Excel tables with raw and Benjamini-Hochberg adjusted P values). 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. Dedu-Honghua-7-Wei San; hepatic fibrosis; network pharmacology; molecular docking; molecular dynamics simulation; Mongolian medicine; carbon tetrachloride Jiuwang Yu PUBLIC https://creativecommons.org/licenses/by/4.0/ dataset Science Data Bank