Aiko Muraishi

Chaperone, a DataFrame-based framework and agent harness for protein design tools, cut tokens 86% and GPU-hours 64% while raising pass rate from 6% to 12%.

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.

An all-atom diffusion model using a 14-atom residue representation and sparse U-Net architecture accelerates biomolecular design 10-fold, enabling experimentally validated DNA-binding proteins and multi-turnover cysteine hydrolases.