Yasuhiro Oda

COPAL uses an ensemble of protein-ligand co-folding models to predict preferred AHL ligands for LuxR receptors, achieving higher accuracy than individual models.

The paper compares a reduced-genome Rhodopseudomonas strain to others, finding it retains core metabolic versatility but lacks genes for high-affinity transport and biodegradation.

The paper identifies adenine as a cross-fed metabolite between Rhodopseudomonas palustris and E. coli, revealing a purine salvage bottleneck mechanism.