Success rate (AlphaFold3 filter) of Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1 on Bennett VHH design target Influenza Hemagglutinin
5% Success rate (AlphaFold3 filter)
Methods
- Tested configuration
- Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1
- Protocol
- Bennett VHH computational success rate under an AlphaFold3 filter
- Dataset
- Bennett VHH design target Influenza Hemagglutinin
- Procedure
- Bennett VHH computational success rate under an AlphaFold3 filter
- Evaluation
- Fine-tuned RFdiffusion VHH computational success rate against H1 stem, AlphaFold3 filter
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source: No interval is printed.
- Evidence
- Author-reported evaluation · source checkedBennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'H1 stem' (Designs screened = 96), column 'Success rate (%) (AF3)'
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- Not reported
- Adaptation
- AlphaFold3 filter
- Scoring implementation
- Share of designs passing the stated structural and confidence thresholds
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
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.
2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 5.0 Individual claims | Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) Supplementary Methods Table 6, row 'H1 stem' (Designs screened = 96), column 'Success rate (%) (AF3)' 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 | source checked ["source-hash-verification","independent-cell-check","ai-assisted-source-review"] · 2026-10-22T15:00:00Z author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsReviewed 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. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
| Reported result 5.0 Individual claims | Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 Supplementary Methods Table 6, row 'H1 stem' (Designs screened = 96), column 'Success rate (%) (AF3)' 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 | source checked ["source-hash-verification","independent-cell-check","ai-assisted-source-review"] · 2026-10-22T15:00:00Z author reported Audit detailsReviewed 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. Field: 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 Extraction artifact SHA-256: |
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: uc-binder-20261022-result-bennett-h1stem-spr-insilico-af3-af3
- metric
- success-rate
- metric direction
- higher
- metric qualifier
- AlphaFold3 filter
- missing metadata
- uncertainty: note: No interval is printed.; reason: unreported
- numeric value
- 5.0
- printed value
- 5.0
- review
- artifact sha256: f5d4fc4f3a65a2dc3ab696e165bb86bf150b2437cdc1a7046cfbecae8ccab05c; method: source-hash-verification; 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
- source locator
- Supplementary Methods Table 6, row 'H1 stem' (Designs screened = 96), column 'Success rate (%) (AF3)'
- unit
- percent
- unit detail
- percent of designs predicted