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
- Scandinavian Journal of Statistics editors reflect on publishing in the age of generative AI — michaelchchoi · 2026-11-11
- Proving LLM backdoor-safety without revealing weights: ZKML over formal methods — DimitrisPapail · 2026-11-11
- Claude Opus 5.5 runs an architecture search and finds AttnRes-Canon, a new top Transformer design — SonglinYang4 · 2026-11-11
- 5 research habits worth knowing: read papers backwards, reproduce first, wire coding agents via MCP — cneuralnetwork · 2026-11-11
- Running Qwen2.5-Coder-3B on Android: Jupyter + Pydantic Evals on-device eval pipeline — alex_b3b · 2026-11-11
- cloneofsimo releases a video explaining determinantal point processes — cloneofsimo · 2026-11-11