{ "id": "AIBD-0046", "title": "RFdiffusion-designed scaffolds let an unaffiliated group solve four small-protein cryo-EM structures", "summary": "A Shandong University team used RFdiffusion and ProteinMPNN scaffolds in a trimbody fiducial to solve four small-protein structures at 2.29 to 2.62 angstroms.", "date_observed": "2026-02-24", "date_basis": "unassessed", "date_precision": "unassessed", "benefit_status": null, "source_collection": null, "source_entry": null, "account": "RFdiffusion is a generative model of protein backbones from the University of Washington Institute for Protein Design. It was published in Nature on 11 July 2023 with experimental validation. That validation included a 2.9 angstrom cryo-EM structure of a designed binder-haemagglutinin complex. The structure matched the computational design model to 0.63 angstrom r.m.s.d. On 24 February 2026 an unaffiliated group at Shandong University and collaborating institutes reported in Nature Communications. They used RFdiffusion and ProteinMPNN to design rigid helical-bundle and TAIL domains for a trimbody fiducial. They then determined atomic-resolution cryo-EM structures of four small proteins that are normally intractable. Human Galectin10 came out at 2.62 angstroms and Aequorea coerulescens GFP at 2.29 angstroms. The Nectin4 IgV domain came out at 2.43 angstroms and Escherichia coli LacY at 2.50 angstroms.", "category": "benefit created", "unexpected": false, "purpose": "Generate de novo protein backbones to order, here to build rigid scaffolds that hold a small target protein still for cryo-electron microscopy.", "system": "RFdiffusion (generative protein backbone diffusion model) with ProteinMPNN sequence design", "model_version": "RFdiffusion", "developer": "University of Washington Institute for Protein Design (Baker lab)", "deployer": "Shandong University and collaborating institutes", "location": "Jinan, China", "domain": "Structural biology / de novo protein design", "segment": null, "benefit_type": "Improved Knowledge Discovery", "taxonomy_note": null, "registry_ids": {}, "ratings": [ { "group": "organizational", "depth": 2, "reason": "The deploying group obtained a reusable fiducial. It yielded four structures between 2.29 and 2.62 angstroms, for proteins that are otherwise difficult targets for cryo-EM." }, { "group": "societal", "depth": 1, "reason": "A methodological advance for structural biology with no identified downstream beneficiaries reported in the source." } ], "ai_role": { "status": "assessed", "statement": "RFdiffusion and ProteinMPNN produced the de novo scaffold domains that make the assembly rigid. The deploying authors are not the tool's developers. They validated the designs experimentally by determining cryo-EM structures at atomic resolution. The designs originated with the deploying group, which used the publicly released model." }, "evidence": [ { "kind": "peer-reviewed study", "citation": "Watson JL, Juergens D, Bennett NR, et al. (2023). De novo design of protein structure and function with RFdiffusion. Nature.", "title": "De novo design of protein structure and function with RFdiffusion", "url": "https://www.nature.com/articles/s41586-023-06415-8", "date": "2023-07-11", "written_by": "makers", "quote": "a generative model of protein backbones that achieves outstanding performance on unconditional and topology-constrained protein monomer design, protein binder design, symmetric oligomer design" }, { "kind": "peer-reviewed study", "citation": "Song J, et al. (2026). Trimbody with rigid AI-designed scaffolds enables atomic-resolution cryo-EM structure determination of small proteins. Nat Commun.", "title": "Trimbody with rigid AI-designed scaffolds enables atomic-resolution cryo-EM structure determination of small proteins", "url": "https://europepmc.org/article/PMC/PMC13043659", "date": "2026-02-24", "written_by": "deployer", "quote": "The de novo 3-helix bundle (H3) and TAIL domains, engineered via RFdiffusion and ProteinMPNN, stabilize the interactions between Nbs and the scaffold" } ], "replication": { "produced_by": [ "Publicly released RFdiffusion and ProteinMPNN models", "A nanobody against each target and a rigid trimbody scaffold design", "Cryo-EM data collection and processing by the deploying group" ], "must_hold": [ "Publicly released RFdiffusion and ProteinMPNN weights", "A nanobody against the target protein", "Cryo-EM data collection and processing capability" ], "echoes": [] }, "paired_incident": null, "headline": "RFdiffusion scaffolds help solve four small-protein structures", "metric": "four small-protein structures at 2.29 to 2.62 angstroms", "comparator": { "against": "earlier DARPin-containing cage fiducials for small proteins", "before": "determined the structure of the cargo protein (GFP) at a local resolution of 3.8 Å but failed to provide a reliable atomic interpretation", "after": "Aequorea coerulescens GFP (2.29 Å)", "basis": "measured", "quote": "The earlier version of the DARPin-containing cage, T33-21, determined the structure of the cargo protein (GFP) at a local resolution of 3.8 Å but failed to provide a reliable atomic interpretation due to the flexibility of the single-helix linker between DARPin and scaffold.", "url": "https://europepmc.org/article/PMC/PMC13043659" }, "later": { "status": "unknown", "date": null, "note": "No later development found.", "quote": null, "url": null }, "value": null, "developer_country": "United States", "deployer_country": "China", "unrated_because": null, "brief_notes": null, "brief": null, "revisions": [ { "date": "2026-10-20", "change": "Record drafted from the cited sources.", "source": null, "editor": "AIBD" }, { "date": "2026-10-20", "change": "Replaced the conflated cryo-EM figure in the account with the paper's own two numbers, a 2.9 angstrom map of the designed binder-haemagglutinin complex and a 0.63 angstrom r.m.s.d. to the design model, because the record had presented 0.63 angstroms as a map resolution.", "source": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10468394/", "editor": "AIBD" }, { "date": "2026-10-21", "change": "Added what the benefit is measured against from the cited sources.", "source": "https://europepmc.org/article/PMC/PMC13043659", "editor": "AIBD" }, { "date": "2026-10-21", "change": "Country of the developer and the deployer added from the organization's own site or a registry.", "source": "https://www.ipd.uw.edu/contact/; https://en.wikipedia.org/wiki/Shandong_University", "editor": "AIBD" }, { "date": "2026-10-21", "change": "Prose pass: a rating reason, account, the system's part rewritten in shorter sentences with abbreviations expanded; facts, figures and quotations unchanged.", "source": null, "editor": "AIBD" } ], "confidence": "claimed", "shade": "low", "claim_status": "The deployer's account", "claim_basis": "Sources: the makers' peer-reviewed study and the deployer's peer-reviewed study. 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