Supplementary Dataset for: Integrative Multi-Omics, Network Pharmacology, and Molecular Simulation of Herbal Compounds Targeting Immune Tolerance Mechanisms in Food Allergy

The supplementary materials for the article provide datasets, analytical results, and methodological details that support the findings in the main manuscript.

These materials include:

SI 1. Herbal Compounds and Genes Identified from Literature and DatabasesA comprehensive list of herbal bioactive compounds was compiled from publicly available databases and literature sources for the network pharmacology analysis.

SI2. GO and KEGG AnalysisThe file contains the results of Gene Ontology enrichment analysis, showing the biological processes, molecular activities, and cellular locations associated with the identified target genes in this study. KEGG pathways are significantly enriched for the candidate targets associated with immune tolerance mechanisms in food allergy.

SI3. Molecular Simulation Parameters and ResultsThe file provides detailed simulation parameters and stability metrics. These include RMSD, RMSF, radius of gyration, hydrogen bonds, and binding free energy analysis for selected compound–protein complexes.

Supplementary MethodsThis section provides detailed methodological procedures supporting the analyses described in the main manuscript. It includes comprehensive descriptions of the data collection and preprocessing steps, compound and target identification, disease-related gene retrieval, protein–protein interaction (PPI) network construction, Gene Ontology (GO) and KEGG pathway enrichment analyses, and the construction of compound–target–pathway networks. Additionally, detailed procedures for molecular docking and molecular dynamics simulations are described, including software tools, parameter settings, and evaluation criteria used in the study. These methodological details are provided to ensure transparency, reproducibility, and facilitate further validation or extension of the analyses.