Relevance of uc-binder-20261022-protocol-bennett-vhh-ecoli-spr-96 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, E. coli expression and single-concentration SPR screen of 96 designs
- Relevance
- Direct evidence
- Endpoint
- Share of designed antibody variable heavy chains confirmed as binders by single-concentration SPR after E. coli expression, out of 96 designs screened per target
The antibody end of the spread, and the strongest corrective in the evidence to the miniprotein hit rates: the same family of methods, on antibody variable domains, gives 0% to 2% where the miniprotein papers report tens of percent. A measured wet-lab outcome with an exact denominator.
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' = SPR; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = SPR 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' = SPR; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = SPR 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' = SPR; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = SPR 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' = SPR; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = SPR 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' = SPR; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = SPR 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' = SPR; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = SPR 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' = SPR; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = SPR 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' = SPR; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = SPR 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 by single-concentration SPR after E. coli expression, out of 96 designs screened per 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' = SPR; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = SPR 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 by single-concentration SPR after E. coli expression, out of 96 designs screened per 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' = SPR; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = SPR 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-ecoli-spr-96
- citation locators
- locator: Supplementary Methods Table 6, rows with 'Initial screening method' = SPR; source id: uc-binder-20261022-source-bennett-si; locator: Supplementary Methods Table 6, rows with 'Initial screening method' = SPR; 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 miniprotein hit rates as a method ranking. The modality is different and so is the assay.; Read the IL7R 0% as a measured zero over 96 designs, not as a missing value.; The main text states 95 designs per target while Table 6 prints 96; the table value is recorded.
- endpoint
- Share of designed antibody variable heavy chains confirmed as binders by single-concentration SPR after E. coli expression, out of 96 designs screened per target
- field
- links:assessed_by:uc-binder-20261022-protocol-bennett-vhh-ecoli-spr-96
- headline metric
- hit-rate
- limitations
- Developer-reported: the authors fine-tuned RFdiffusion, chose the targets, chose the filter and ran the screens.; The designs tested passed the authors' own fine-tuned RoseTTAFold2 filter at a setting the table caption calls 'likely not the most predictive', so design and selection are coupled and the paper itself attributes the low rates partly to the filter.; No numeric SPR response or affinity threshold is printed for what counts as a confirmed binder.; No conventional comparator (immunisation, hybridoma or library selection) was run on these targets.; No uncertainty is printed.; Two design targets, RSV-F site I and HIV Env, have no printed outcome at all.
- rationale
- The antibody end of the spread, and the strongest corrective in the evidence to the miniprotein hit rates: the same family of methods, on antibody variable domains, gives 0% to 2% where the miniprotein papers report tens of percent. A measured wet-lab outcome with an exact denominator.
- 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-spr; uc-binder-20261022-eval-bennett-il7r-spr; uc-binder-20261022-eval-bennett-tcdb-spr
- revision
- 1
- source locator
- uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, rows with 'Initial screening method' = SPR; uc-binder-20261022-source-bennett: Supplementary Methods Table 6, rows with 'Initial screening method' = SPR
- stratum label
- Fine-tuned RFdiffusion VHHs, 96 designs per target by SPR
- stratum order
- 1
- value
- uc-binder-20261022-protocol-bennett-vhh-ecoli-spr-96
- pins
- record id: uc-binder-20261022-eval-bennett-h1stem-spr; fields: status; links; attributes.origin; attributes.comparison; sha256: 9797917995b91c0d6769afc710004c05f3ff0be2c09c4414b22e23912a342197; record id: uc-binder-20261022-eval-bennett-il7r-spr; fields: status; links; attributes.origin; attributes.comparison; sha256: b73458d489ff3833130098fb043927517d1751d166fec9aa2979dd695731ebe6; record id: uc-binder-20261022-eval-bennett-tcdb-spr; fields: status; links; attributes.origin; attributes.comparison; sha256: 7a3c03eefde52fc125878dea3ec13af4c0280adb85891de1d08113dd0005f804; record id: uc-binder-20261022-protocol-bennett-vhh-ecoli-spr-96; fields: status; name; description; facets; source_ids; links; attributes; sha256: e800496caa6ceef7f623708dcbd25b0e82b022b399b38c47b8ad35bf70fad45d; record id: uc-binder-20261022-result-bennett-h1stem-spr-binders; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: f43e209e360cbd3d3247b99a167349e6a5291a95ef68d3849e142673ccf11e09; record id: uc-binder-20261022-result-bennett-h1stem-spr-hitrate; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: b433dbb83da7c918fdb7763d6694e4386f907b080fd1e696ba0a4033dbe1ab5c; record id: uc-binder-20261022-result-bennett-il7r-spr-binders; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 3a0b3a5d39f1d0d2c68e4fe73da1cf4d253462b0823b069ef7afd8ba017e38ad; record id: uc-binder-20261022-result-bennett-il7r-spr-hitrate; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 91ecab6fa27b9c2ddc4b647f19491046bdce11dbdca69f305a88303024db095d; record id: uc-binder-20261022-result-bennett-tcdb-spr-binders; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 5e6e1eb03d114a671c51c5789fe9a83ea5ed65c37dbd3788e076fa334c0aa623; record id: uc-binder-20261022-result-bennett-tcdb-spr-hitrate; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: f3fefca231cb36ca541288b26b85beba079c9c066df12b3bd6d15c4c391a50ca; record id: uc-binder-20261022-source-bennett; fields: status; attributes.artifact_sha256; sha256: 67767c4e09155df3488e2ce80dcb47410db9ba4912be584cd0fab0d01bf6d077; record id: uc-binder-20261022-source-bennett-si; fields: status; attributes.artifact_sha256; sha256: ce65600570751c68a989080759fe025cbebbaa414d8f6416e6870bb7f23afbfd; record id: use-case-de-novo-binder-design; fields: status; name; description; facets; attributes.question; attributes.decision; attributes.inputs; attributes.output; attributes.exclusions; attributes.setting; attributes.clinical_scope; attributes.intended_users; sha256: b5a0012d1b0f02d6bd7466b7308123b26e676eda8ef54d706c865bb3f777e5b9