ModelSEED Biochemistry Database
The reference biochemistry database for genome-scale metabolic modeling
The ModelSEED Biochemistry Database is the reference set of compounds and reactions — with structures, thermodynamics, and mass/charge balancing — used to reconstruct, compare, and analyze genome-scale metabolic models across plants, fungi, and microbes. I lead its curation, including large-scale structure and formula curation across the ~9,000 reactions and ~6,500 compounds that underpin the ModelSEEDTemplates and PlantSEED.
- Role: first author of the database paper (Nucleic Acids Research, 2021); ongoing curation lead.
- Highlights: mass-balance exclusion mechanism for R-group compounds; stereochemistry-preservation safeguards; integration with a PubChem validation pipeline.
- Links: GitHub · see the publications page.