This page provides curated databases and tools used in our laboratory for the identification, validation, and mechanistic analysis of food-derived bioactive compounds.
Plant & Natural Product Databases
KNApSAcK Family
Plant–metabolite relationships and literature-supported phytochemicals
Dr. Duke’s Phytochemical Database
Food-based phytochemicals and their biological activities
Natural Products Atlas (NPAtlas)
Structures and classifications of natural compounds
Traditional Chinese Medicine Systems Pharmacology (TCMSP)
A database for collecting natural compounds and ADME properties (oral bioavailability, drug-likeness) and predicted targets
LC-MS & Metabolomics Tools
ChemCalc
Accurate mass to molecular formula prediction
METLIN Metabolite Database
High-resolution tandem MS database for metabolite identification
MassBank
Public repository of mass spectra for small chemical compounds
GNPS
MS/MS spectral networking and annotation platform
Food & Nutritional Databases
FooDB
Comprehensive database of food components and bioactives
Human Metabolome Database (HMDB)
Metabolomic and chemical information on human metabolites
In Silico & Structural Biology Tools
PubChem
Chemical structures, properties, and biological activities
RCSB Protein Data Bank (PDB)
Three-dimensional structures of proteins and nucleic acids for docking
AutoDock Vina
Open-source molecular docking engine
CB-Dock2
Cavity detection-guided docking web tool
AlphaFold
AI-predicted 3D structures for proteins, useful when experimental structures are unavailable
SwissTargetPrediction
Prediction of likely protein targets for small molecules based on chemical similarity
Target Prediction Databases
BATMAN-TCM
An online tool for predicting compound–target interactions and assigning potential protein targets
SwissTargetPredicition
Predicts likely human protein targets of small molecules using chemical similarity; commonly used to expand and validate target lists for natural compounds
Disease-Related Gene Databases
DisGeNET
Integrates gene–disease association data from multiple sources; used to identify disease-relevant genes for network construction
GeneCards
Comprehensive database of annotated human genes including disease relevance scores, expression profiles and functional summaries
OMIM
Authoritative compendium of human genes and genetic phenotypes, supporting confirmation of gene–disease relevance
Network Construction and Analysis
jvenn
Web tool for generating Venn diagrams of overlapping gene/target lists, useful for identifying common targets between compounds and diseases
STRING — Protein–Protein Interaction Networks
Generates protein–protein interaction networks based on curated and predicted interactions; essential for network pharmacology and hub gene analysis
DAVID — Functional Annotation & Enrichment
Functional enrichment tool for Gene Ontology and KEGG pathway analysis of gene sets
Disclaimer
The links provided are for reference only. We are not responsible for the content or accuracy of external websites.