{"id":14,"date":"2026-01-11T12:27:12","date_gmt":"2026-01-11T12:27:12","guid":{"rendered":"https:\/\/rosdires.org\/?page_id=14"},"modified":"2026-02-05T05:42:57","modified_gmt":"2026-02-05T05:42:57","slug":"usefullinks","status":"publish","type":"page","link":"https:\/\/rosdires.org\/index.php\/usefullinks\/","title":{"rendered":"Useful Links"},"content":{"rendered":"\n
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This page provides curated databases and tools used in our laboratory for the identification, validation, and mechanistic analysis of food-derived bioactive compounds.<\/em><\/p>\n<\/blockquote>\n\n\n\n


Plant & Natural Product Databases<\/strong><\/p>\n\n\n\n

KNApSAcK Family<\/a><\/strong>
Plant\u2013metabolite relationships and literature-supported phytochemicals<\/em>
Dr. Duke\u2019s Phytochemical Database<\/a><\/strong>
Food-based phytochemicals and their biological activities<\/em>
Natural Products Atlas (NPAtlas)<\/a><\/strong>
Structures and classifications of natural compounds<\/em>
Traditional Chinese Medicine Systems Pharmacology (TCMSP)<\/a><\/strong>
A database for collecting natural compounds and ADME properties (oral bioavailability, drug-likeness) and predicted targets<\/em><\/p>\n\n\n\n


LC-MS & Metabolomics Tools<\/strong><\/strong><\/p>\n\n\n\n

ChemCalc<\/a><\/strong>
Accurate mass to molecular formula prediction<\/em>
METLIN Metabolite Database<\/strong> <\/a>
High-resolution tandem MS database for metabolite identification<\/em>
MassBank<\/a><\/strong> 
Public repository of mass spectra for small chemical compounds<\/em>
GNPS<\/a><\/strong>
MS\/MS spectral networking and annotation platform<\/em><\/p>\n\n\n\n


Food & Nutritional Databases<\/strong><\/strong><\/p>\n\n\n\n

FooDB<\/a><\/strong> 
Comprehensive database of food components and bioactives<\/em>
Human Metabolome Database (HMDB)<\/a><\/strong> 
Metabolomic and chemical information on human metabolites<\/em><\/p>\n\n\n\n


In Silico & Structural Biology Tools<\/strong><\/strong><\/strong><\/p>\n\n\n\n

PubChem<\/a><\/strong>\u00a0
Chemical structures, properties, and biological activities<\/em>
RCSB Protein Data Bank (PDB)<\/a><\/strong>\u00a0
Three-dimensional structures of proteins and nucleic acids for docking<\/em>
AutoDock Vina<\/a><\/strong>
Open-source molecular docking engine<\/em>
CB-Dock2<\/strong>\u00a0<\/a>
Cavity detection-guided docking web tool<\/em>
AlphaFold<\/a> <\/strong>
AI-predicted 3D structures for proteins, useful when experimental structures are unavailable<\/em>
SwissTargetPrediction<\/a><\/strong>
Prediction of likely protein targets for small molecules based on chemical similarity<\/em><\/p>\n\n\n\n


Target Prediction Databases<\/strong><\/p>\n\n\n\n

BATMAN-TCM<\/a><\/strong>
An online tool for predicting compound\u2013target interactions and assigning potential protein targets<\/em>
SwissTargetPredicition<\/a><\/strong>
Predicts likely human protein targets of small molecules using chemical similarity; commonly used to expand and validate target lists for natural compounds<\/em><\/p>\n\n\n\n


Disease-Related Gene Databases<\/strong><\/p>\n\n\n\n

DisGeNET<\/a><\/strong>
Integrates gene\u2013disease association data from multiple sources; used to identify disease-relevant genes for network construction<\/em>
GeneCards<\/a><\/strong>
Comprehensive database of annotated human genes including disease relevance scores, expression profiles and functional summaries<\/em>
OMIM<\/a><\/strong>
Authoritative compendium of human genes and genetic phenotypes, supporting confirmation of gene\u2013disease relevance<\/em><\/p>\n\n\n\n


Network Construction and Analysis<\/strong><\/p>\n\n\n\n

jvenn<\/a><\/strong>
Web tool for generating Venn diagrams of overlapping gene\/target lists, useful for identifying common targets between compounds and diseases<\/em>
STRING \u2014 Protein\u2013Protein Interaction Networks<\/strong><\/a><\/strong>
Generates protein\u2013protein interaction networks based on curated and predicted interactions; essential for network pharmacology and hub gene analysis<\/em>
DAVID \u2014 Functional <\/strong><\/a>Annotation<\/a><\/strong> & Enrichment<\/strong><\/a><\/strong>
Functional enrichment tool for Gene Ontology and KEGG pathway analysis of gene sets<\/em><\/p>\n\n\n\n

Disclaimer<\/strong><\/p>\n\n\n\n

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The links provided are for reference only. We are not responsible for the content or accuracy of external websites.<\/p>\n<\/blockquote>\n\n\n\n

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<\/i>Love<\/span>0<\/span><\/span><\/a> <\/i> <\/i>