Relevance of uc-binder-20261022-protocol-bennett-vhh-yeast-display-9000 to "Which computational design workflow produces binders that work when they are made and tested?"
- Use case
- Design a new binder to a chosen target
- Assessed by
- Bennett VHH design, yeast surface display screen of 9,000 designs with SPR confirmation
- Relevance
- Direct evidence
- Endpoint
- Share of designed antibody variable heavy chains confirmed as binders after yeast surface display screening of 9,000 designs per target with SPR confirmation
The largest denominators in the whole evidence set, and the clearest demonstration that effort and hit rate are not the same claim: 9,000 designs per target yield 0.01% to 0.2%. The influenza H1 stem target was screened both ways, so this protocol and the 96-design SPR protocol can be read side by side on one target.
3 reviewed evaluations
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
40 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Citation locations2 values
| Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature, version of record; Europe PMC JATS full text for PMC12727541 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Citation locations2 values
| Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF 41586_2025_9721_MOESM1_ESM.pdf, 129 pages, InDesign 17.4, ModDate 2026-09-15 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of the Supplementary Information PDF as extracted from one retrieval of the supplementary archive on 2026-10-22. The archive itself was truncated (103,690,987 bytes, SHA-256 6b1bd61ba4d69d5393f56e0e0d12bb4349b45ce12496a1d3e6a5a8467c39203a) and is not the pinned artifact. Archive member: 41586_2025_9721_MOESM1_ESM.pdf, extracted from the Europe PMC supplementaryFiles archive for PMC12727541 |
| Comparison group antibody-binder-hit-rates Context-only references | Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature, version of record; Europe PMC JATS full text for PMC12727541 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison group antibody-binder-hit-rates Context-only references | Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF 41586_2025_9721_MOESM1_ESM.pdf, 129 pages, InDesign 17.4, ModDate 2026-09-15 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of the Supplementary Information PDF as extracted from one retrieval of the supplementary archive on 2026-10-22. The archive itself was truncated (103,690,987 bytes, SHA-256 6b1bd61ba4d69d5393f56e0e0d12bb4349b45ce12496a1d3e6a5a8467c39203a) and is not the pinned artifact. Archive member: 41586_2025_9721_MOESM1_ESM.pdf, extracted from the Europe PMC supplementaryFiles archive for PMC12727541 |
| Comparison title Antibody variable-domain hit rates by target Context-only references | Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature, version of record; Europe PMC JATS full text for PMC12727541 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison title Antibody variable-domain hit rates by target Context-only references | Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF 41586_2025_9721_MOESM1_ESM.pdf, 129 pages, InDesign 17.4, ModDate 2026-09-15 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of the Supplementary Information PDF as extracted from one retrieval of the supplementary archive on 2026-10-22. The archive itself was truncated (103,690,987 bytes, SHA-256 6b1bd61ba4d69d5393f56e0e0d12bb4349b45ce12496a1d3e6a5a8467c39203a) and is not the pinned artifact. Archive member: 41586_2025_9721_MOESM1_ESM.pdf, extracted from the Europe PMC supplementaryFiles archive for PMC12727541 |
Constraints3 values
| Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature, version of record; Europe PMC JATS full text for PMC12727541 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints3 values
| Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF 41586_2025_9721_MOESM1_ESM.pdf, 129 pages, InDesign 17.4, ModDate 2026-09-15 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of the Supplementary Information PDF as extracted from one retrieval of the supplementary archive on 2026-10-22. The archive itself was truncated (103,690,987 bytes, SHA-256 6b1bd61ba4d69d5393f56e0e0d12bb4349b45ce12496a1d3e6a5a8467c39203a) and is not the pinned artifact. Archive member: 41586_2025_9721_MOESM1_ESM.pdf, extracted from the Europe PMC supplementaryFiles archive for PMC12727541 |
| Endpoint Share of designed antibody variable heavy chains confirmed as binders after yeast surface display screening of 9,000 designs per target with SPR confirmation Context-only references | Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature, version of record; Europe PMC JATS full text for PMC12727541 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Endpoint Share of designed antibody variable heavy chains confirmed as binders after yeast surface display screening of 9,000 designs per target with SPR confirmation Context-only references | Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF 41586_2025_9721_MOESM1_ESM.pdf, 129 pages, InDesign 17.4, ModDate 2026-09-15 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of the Supplementary Information PDF as extracted from one retrieval of the supplementary archive on 2026-10-22. The archive itself was truncated (103,690,987 bytes, SHA-256 6b1bd61ba4d69d5393f56e0e0d12bb4349b45ce12496a1d3e6a5a8467c39203a) and is not the pinned artifact. Archive member: 41586_2025_9721_MOESM1_ESM.pdf, extracted from the Europe PMC supplementaryFiles archive for PMC12727541 |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 · Original source · Supplementary Information PDF 41586_2025_9721_MOESM1_ESM.pdf, 129 pages, InDesign 17.4, ModDate 2026-09-15
- Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Original source · Nature, version of record; Europe PMC JATS full text for PMC12727541
Technical metadata and extraction receipts
Stable ID: use-case-mapping-binder-20261022-bennett-vhh-yeast-display-9000
- citation locators
- locator: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD; source id: uc-binder-20261022-source-bennett-si; locator: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD; source id: uc-binder-20261022-source-bennett
- comparison group
- antibody-binder-hit-rates
- comparison title
- Antibody variable-domain hit rates by target
- constraints
- Do not compare these rates with the 96-design SPR rates as if they were the same experiment. On H1 stem the same design campaign gives 1% over 96 designs by SPR and 0.2% over 9,000 by display.; Do not compare with the miniprotein hit rates as a method ranking.; Read each rate with its 9,000-design denominator.
- endpoint
- Share of designed antibody variable heavy chains confirmed as binders after yeast surface display screening of 9,000 designs per target with SPR confirmation
- field
- links:assessed_by:uc-binder-20261022-protocol-bennett-vhh-yeast-display-9000
- headline metric
- hit-rate
- limitations
- Developer-reported.; The designs screened passed the authors' own filter at a setting the table caption calls 'likely not the most predictive'.; No numeric display-signal or affinity threshold is printed for what counts as a confirmed binder.; No conventional comparator was run, although the discussion contrasts the approach with yeast display selection from random libraries.; No uncertainty is printed.
- rationale
- The largest denominators in the whole evidence set, and the clearest demonstration that effort and hit rate are not the same claim: 9,000 designs per target yield 0.01% to 0.2%. The influenza H1 stem target was screened both ways, so this protocol and the 96-design SPR protocol can be read side by side on one target.
- reason
- Add measured de novo binder design outcomes from the 2026-10-22 use-case evidence pass (#176).
- relevance
- direct
- review
- artifact sha256: f5d4fc4f3a65a2dc3ab696e165bb86bf150b2437cdc1a7046cfbecae8ccab05c; method: scope-review; independent-cell-check; ai-assisted-source-review; method note: The supplementary archive now returns 107,210,814 bytes and extracts cleanly with unzip, where the extraction pass received a truncated 103,690,987-byte archive it had to stream with bsdtar. The pinned member hash is what matters and it matched exactly: 41586_2025_9721_MOESM1_ESM.pdf is f5d4fc4f3a65a2dc3ab696e165bb86bf150b2437cdc1a7046cfbecae8ccab05c. Own text layer with pdftotext -layout (poppler 26.08.0), reproducing 3,582 lines; Supplementary Methods Tables 5 and 6 read cell by cell.; note: Reviewed in docs/reviews/use-cases/binder-2026-10-22.md. Automated AI review of the source transcription only; it is not human scientific review and nothing here was reproduced experimentally.; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12727541/supplementaryFiles; reviewed at: 2026-10-22T15:00:00Z; reviewer: claude; reviewer note: Claude review agent, independent of the extraction agent; no human review claimed; scope: Endpoint fit, relevance grade, constraints, limitations, comparison grouping and the evaluations listed in reviewed_evaluations.
- reviewed evaluations
- uc-binder-20261022-eval-bennett-h1stem-ysd; uc-binder-20261022-eval-bennett-rbd-ysd; uc-binder-20261022-eval-bennett-rsv3-ysd
- revision
- 1
- source locator
- uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = YSD
- stratum label
- Fine-tuned RFdiffusion VHHs, 9,000 designs per target by yeast display
- stratum order
- 2
- value
- uc-binder-20261022-protocol-bennett-vhh-yeast-display-9000
- pins
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