Andrew Freiburger

This update expands the ModelSEED Biochemistry Database to roughly 46,000 compounds, 56,000 reactions and 37,000 metabolic structures, widens thermodynamic handling from two sources to four (group contribution, eQuilibrator 3.0, dGPredictor and experimental values) each kept with its own uncertainty, assigns gold, silver or bronze evidence grades to about 33,000 reactions, and releases reaction directions predicted by an ensemble of large language models alongside a new conflict-resolution pipeline that documents structural choices across sources.

This update expands the ModelSEED Biochemistry Database to roughly 46,000 compounds, 56,000 reactions and 37,000 metabolic structures, widens thermodynamic handling from two sources to four (group contribution, eQuilibrator 3.0, dGPredictor and experimental values) each kept with its own uncertainty, assigns gold, silver or bronze evidence grades to about 33,000 reactions, and releases reaction directions predicted by an ensemble of large language models alongside a new conflict-resolution pipeline that documents structural choices across sources.