Davi Nakajima An

CaGE alternates guided structure prediction with sequence redesign, fading guidance each cycle, so sequences recover complex catalytic sites unaided; designed nonheme-iron and PLP-dependent enzymes were active.

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 introduces a method to map linker-length landscapes for coupling synthetic CID systems to molecular readouts, showing linker length strongly affects coupling efficiency.

The paper uses deep learning to predict protein-protein interactions in E. coli's outer membrane biogenesis pathway, revealing new insights into protein complex structures and functions.

The paper adapts AlphaFold2 models to predict structures of multimeric protein complexes and introduces metrics for predicting direct protein-protein interactions.