Karthik Raman

Enzyme function prediction has relied on homology search or on mapping enzymes to known reactions, so it cannot output a reaction absent from its training data. A model conditioned on enzyme sequence and AlphaFold structure and generating a reaction metabolite by metabolite recovers the complete correct reaction for 25.0% of metabolite-recombination test pairs within 400 sampled candidates on the reaction-disjoint EnzymeMap_x benchmark, and for only 1.6% of pairs containing a metabolite unseen in training. A matched ablation finds no measurable effect of the structural channel on exact recovery; vocabulary coverage and chemical initialisation account for most of the gain.

Enzyme function prediction has relied on homology search or on mapping enzymes to known reactions, so it cannot output a reaction absent from its training data. A model conditioned on enzyme sequence and AlphaFold structure and generating a reaction metabolite by metabolite recovers the complete correct reaction for 25.0% of metabolite-recombination test pairs within 400 sampled candidates on the reaction-disjoint EnzymeMap_x benchmark, and for only 1.6% of pairs containing a metabolite unseen in training. A matched ablation finds no measurable effect of the structural channel on exact recovery; vocabulary coverage and chemical initialisation account for most of the gain.