Baker lab de novo designs cysteine proteases: 13 of 69 designs cleave paired substrates
AllThingsApx · x · 2026-09-26
David Baker's lab at the UW Institute for Protein Design posted a bioRxiv preprint on de novo design of cysteine proteases:
- Pipeline: RFD2-MI scaffolds the catalytic atoms plus peptide substrate, ProteinMPNN co-designs enzyme and substrate sequences, and AlphaFold3 validates both bound and unbound structures.
- Results: 13 of 69 selected designs successfully cleaved their paired substrates.
- Open source: The team released the design pipeline and analysis scripts (model weights not bundled), plus notebooks for kinetics assays and mammalian-cell imaging.
A notable AI-for-Science advance in computational enzyme design.
More from Research
- Open-source stack plans fuel-optimal A320 routes, could save thousands per transatlantic flight — JeremyCMorgan · 2026-09-26
- Preprint: selecting for 'freedom of function' beats likelihood-based evolution on 5 benchmarks — burny_tech · 2026-09-26
- Researchers gave LLMs "brain damage" and found they mimic human aphasia symptoms — coryshain · 2026-09-26
- Simulated fruit fly brain is learning to fight its way through Battletoads — Inevitable_Emu2722 · 2026-09-26
- NSF Robotics Meeting Workshop: Four Researchers on Learning, Generalization and Physical Intelligence — YuXiang_IRVL · 2026-09-26
- Xiaomi MiMo open-sources its RL environments and training code on a fork of verl — eliebakouch · 2026-09-26