{"schema":"postcutoff/event@1","as_of":"2026-11-13T13:49:00+01:00","url":"https://postcutoff.com/e/2023-07-11-rfdiffusion-protein-design/","md":"https://postcutoff.com/e/2023-07-11-rfdiffusion-protein-design/index.md","disclosure":{"written_by":"AI agents (Claude Opus 5.5 in Claude Code)","editor":"human editor","policy":"https://postcutoff.com/about/"},"license":null,"id":"2023-07-11-rfdiffusion-protein-design","date":"2023-07-11","date_precision":"day","short_title":"RFdiffusion: diffusion models design new proteins that work in the lab","deck":null,"takeaway":"David Baker's lab (Nature, July 2023) fine-tuned RoseTTAFold as a diffusion model to generate new protein backbones for binders, symmetric assemblies and metal-binding sites.","category":"science","category_label":"Science & math","importance":4,"confidence":"high","status":{"key":"confirmed","labels":["Result confirmed"]},"sources":[{"n":1,"title":"De novo design of protein structure and function with RFdiffusion (Nature)","url":"https://www.nature.com/articles/s41586-023-06415-8","type":"paper","group":"primary","domain":"nature.com"},{"n":2,"title":"Baker Lab: RFdiffusion now free and open source","url":"https://www.bakerlab.org/2023/03/30/rf-diffusion-now-free-and-open-source/","type":"official","group":"primary","domain":"bakerlab.org"},{"n":3,"title":"IPD: RFdiffusion3 now available","url":"https://www.ipd.uw.edu/2025/12/rfdiffusion3-now-available/","type":"official","group":"primary","domain":"ipd.uw.edu"}],"official":3,"filed":"2026-09-29","updated":"2026-09-29","orgs":["University of Washington Institute for Protein Design"],"title":"RFdiffusion: diffusion models design new proteins that work in the lab","summary":"David Baker's lab (Nature, July 2023) fine-tuned RoseTTAFold as a diffusion model to generate new protein backbones for binders, symmetric assemblies and metal-binding sites. Hundreds of designs were experimentally characterised. A cryo-EM structure of a designed binder bound to influenza haemagglutinin was nearly identical to the design model.","key_facts":["Nature, 11 Jul 2023; code released free and open-source in 2023","Designs: protein binders, symmetric oligomers, enzyme active-site scaffolds, metal-binding proteins","Successors: RFdiffusion2 (Nature Methods, Jan 2026: scaffolds for all 41 benchmark active sites vs 16 before) and RFdiffusion3 (open-sourced Dec 2025)","Part of the work recognised by the 2024 Nobel Prize in Chemistry (Baker)"],"key_numbers":[],"tags":["biology","protein-design","diffusion","open-source"],"science":{"field":"biology","subfield":"de novo protein design","problem":"Designing proteins with specified shapes and functions from scratch","result":"A general generative model whose protein designs fold and bind as intended at high experimental success rates.","open_since":"","ai_system":["RFdiffusion"],"human_role":"Human-designed system; humans select and test designs","verification":{"key":"peer-review","label":"Peer-reviewed","text":"Peer-reviewed in Nature; lab-validated incl. cryo-EM"},"status":"confirmed","shock":""},"body_md":"## What happened\n\nBy adapting image-generation-style diffusion to protein structures, the Baker lab made protein design largely a matter of generating and filtering candidates on computers.\n\n## Why it matters\n\nIt became the workhorse of AI protein design, underlying AI antivenoms, antibodies and enzymes.","disputed":[],"related":[{"id":"2025-11-05-ai-designed-antibodies-rfdiffusion","url":"https://postcutoff.com/e/2025-11-05-ai-designed-antibodies-rfdiffusion/","date":"2025-11-05","date_precision":"month","short_title":"Baker lab designs antibodies from scratch with atomic accuracy using RFdiffusion","deck":null,"takeaway":"Computational antibody design could replace months of animal immunisation and library screening in drug discovery.","category":"science","category_label":"Science & math","importance":3,"confidence":"high","status":{"key":"confirmed","labels":["Result confirmed"]},"sources":3,"official":2,"filed":"2026-09-29","updated":"2026-09-29","orgs":["University of Washington Institute for Protein Design"]},{"id":"2025-01-15-ai-designed-antivenom","url":"https://postcutoff.com/e/2025-01-15-ai-designed-antivenom/","date":"2025-01-15","date_precision":"day","short_title":"AI-designed proteins neutralise deadly snake-venom toxins and protect mice","deck":null,"takeaway":"Snakebite kills tens of thousands of people a year, mainly in poor regions.","category":"science","category_label":"Science & math","importance":3,"confidence":"high","status":{"key":"confirmed","labels":["Result confirmed"]},"sources":3,"official":2,"filed":"2026-09-29","updated":"2026-09-29","orgs":["University of Washington Institute for Protein Design","Technical University of Denmark"]},{"id":"2024-10-09-nobel-chemistry-alphafold","url":"https://postcutoff.com/e/2024-10-09-nobel-chemistry-alphafold/","date":"2024-10-09","date_precision":"day","short_title":"Nobel Prize in Chemistry for protein design and AlphaFold","deck":null,"takeaway":"Confirmed AI as a tool of first-rank scientific discovery, less than four years after AlphaFold 2.","category":"milestone","category_label":"Milestones","importance":5,"confidence":"high","status":{"key":"confirmed","labels":["Result confirmed"]},"sources":3,"official":2,"filed":"2026-09-29","updated":"2026-09-29","orgs":["Royal Swedish Academy of Sciences","Google DeepMind","University of Washington"]}],"people":[],"posts":[],"videos":[],"models":[],"changes":[{"date":"2026-09-29","type":"filed","text":"Created"}],"provenance":{"agents":[{"model":"Claude Opus 5.5","maker":"Anthropic","tool":"Claude Code"}],"filed":"2026-09-29","run":null,"sources_read":null,"updated":"2026-09-29","human_review":null,"version":{"date":"2026-10-04"}},"gaps":[{"model_id":"gpt-6-astra","name":"GPT-6 Astra","cutoff":"2026-04","days_after":null,"in_training_data":true},{"model_id":"claude-opus-5-5","name":"Claude Opus 5.5","cutoff":"2026-06","days_after":null,"in_training_data":true},{"model_id":"gemini-4-hydrogen","name":"Gemini 4 Hydrogen","cutoff":"2026-03","days_after":null,"in_training_data":true},{"model_id":"grok-4-7","name":"Grok 4.7","cutoff":"2026-05","days_after":null,"in_training_data":true}],"short_url":"https://postcutoff.com/s/rfdiffusion-diffusion-design-new"}