Evaluation

Fine-tuned RFdiffusion VHH computational success rate against TcdB, AlphaFold3 filter

Developer-reported in silico filter pass rate transcribed from the pinned supplementary table; not a measured outcome and not reproduced.

Evaluation results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
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 TcdB	27.5% Success rate (AlphaFold3 filter) percent · higher Uncertainty: Not reported by the source: No interval is printed. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against TcdB, AlphaFold3 filter uc-binder-20261022-protocol-bennett-insilico-af3-success Aggregation: Not reported Bennett 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 'TcdB' (Designs screened = 96), column 'Success rate (%) (AF3)'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

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Evaluation procedure

Bennett VHH computational success rate under an AlphaFold3 filter

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 TcdB

origin: Author-reported evaluation
configuration: Nature 2025 version of record; Supplementary Methods Table 6
adaptation: AlphaFold3 filter
aggregation: Per target
budget: 200 backbones designed per target
dataset version: TcdB, Supplementary Methods Table 5 epitope
inputs: Cropped target structure with the Table 5 hotspot residues as the epitope
metric implementation: Share of designs passing the stated structural and confidence thresholds
population: 200 backbones per target, best of 8 ProteinMPNN sequences each
protocol id: uc-binder-20261022-protocol-bennett-insilico-af3-success
split: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Not reported
Adaptation: AlphaFold3 filter
Scoring implementation: Share of designs passing the stated structural and confidence thresholds

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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

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Evidence table

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19 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Comparison: adaptation AlphaFold3 filter Context-only references	Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 Original source ↗ Supplementary Methods Table 6, row 'TcdB' (Designs screened = 96), column 'Success rate (%) (AF3)' Version: Supplementary Information PDF 41586_2025_9721_MOESM1_ESM.pdf, 129 pages, InDesign 17.4, ModDate 2026-09-15 Retrieved: 2026-10-22T12:05:00Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `f5d4fc4f3a65a2dc3ab696e165bb86bf150b2437cdc1a7046cfbecae8ccab05c` 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 Inspected artifact
Comparison: aggregation Per target Context-only references	Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 Original source ↗ Supplementary Methods Table 6, row 'TcdB' (Designs screened = 96), column 'Success rate (%) (AF3)' Version: Supplementary Information PDF 41586_2025_9721_MOESM1_ESM.pdf, 129 pages, InDesign 17.4, ModDate 2026-09-15 Retrieved: 2026-10-22T12:05:00Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `f5d4fc4f3a65a2dc3ab696e165bb86bf150b2437cdc1a7046cfbecae8ccab05c` 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 Inspected artifact
Comparison: budget 200 backbones designed per target Context-only references	Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 Original source ↗ Supplementary Methods Table 6, row 'TcdB' (Designs screened = 96), column 'Success rate (%) (AF3)' Version: Supplementary Information PDF 41586_2025_9721_MOESM1_ESM.pdf, 129 pages, InDesign 17.4, ModDate 2026-09-15 Retrieved: 2026-10-22T12:05:00Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `f5d4fc4f3a65a2dc3ab696e165bb86bf150b2437cdc1a7046cfbecae8ccab05c` 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 Inspected artifact
Comparison: dataset version TcdB, Supplementary Methods Table 5 epitope Context-only references	Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 Original source ↗ Supplementary Methods Table 6, row 'TcdB' (Designs screened = 96), column 'Success rate (%) (AF3)' Version: Supplementary Information PDF 41586_2025_9721_MOESM1_ESM.pdf, 129 pages, InDesign 17.4, ModDate 2026-09-15 Retrieved: 2026-10-22T12:05:00Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `f5d4fc4f3a65a2dc3ab696e165bb86bf150b2437cdc1a7046cfbecae8ccab05c` 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 Inspected artifact
Comparison: inputs Cropped target structure with the Table 5 hotspot residues as the epitope Context-only references	Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 Original source ↗ Supplementary Methods Table 6, row 'TcdB' (Designs screened = 96), column 'Success rate (%) (AF3)' Version: Supplementary Information PDF 41586_2025_9721_MOESM1_ESM.pdf, 129 pages, InDesign 17.4, ModDate 2026-09-15 Retrieved: 2026-10-22T12:05:00Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `f5d4fc4f3a65a2dc3ab696e165bb86bf150b2437cdc1a7046cfbecae8ccab05c` 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 Inspected artifact
Comparison: metric implementation Share of designs passing the stated structural and confidence thresholds Context-only references	Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 Original source ↗ Supplementary Methods Table 6, row 'TcdB' (Designs screened = 96), column 'Success rate (%) (AF3)' Version: Supplementary Information PDF 41586_2025_9721_MOESM1_ESM.pdf, 129 pages, InDesign 17.4, ModDate 2026-09-15 Retrieved: 2026-10-22T12:05:00Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `f5d4fc4f3a65a2dc3ab696e165bb86bf150b2437cdc1a7046cfbecae8ccab05c` 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 Inspected artifact
Comparison: population 200 backbones per target, best of 8 ProteinMPNN sequences each Context-only references	Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 Original source ↗ Supplementary Methods Table 6, row 'TcdB' (Designs screened = 96), column 'Success rate (%) (AF3)' Version: Supplementary Information PDF 41586_2025_9721_MOESM1_ESM.pdf, 129 pages, InDesign 17.4, ModDate 2026-09-15 Retrieved: 2026-10-22T12:05:00Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `f5d4fc4f3a65a2dc3ab696e165bb86bf150b2437cdc1a7046cfbecae8ccab05c` 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 Inspected artifact
Comparison: protocol id uc-binder-20261022-protocol-bennett-insilico-af3-success Context-only references	Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 Original source ↗ Supplementary Methods Table 6, row 'TcdB' (Designs screened = 96), column 'Success rate (%) (AF3)' Version: Supplementary Information PDF 41586_2025_9721_MOESM1_ESM.pdf, 129 pages, InDesign 17.4, ModDate 2026-09-15 Retrieved: 2026-10-22T12:05:00Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `f5d4fc4f3a65a2dc3ab696e165bb86bf150b2437cdc1a7046cfbecae8ccab05c` 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 Inspected artifact
Comparison: split Not reported Context-only references	Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 Original source ↗ Supplementary Methods Table 6, row 'TcdB' (Designs screened = 96), column 'Success rate (%) (AF3)' Version: Supplementary Information PDF 41586_2025_9721_MOESM1_ESM.pdf, 129 pages, InDesign 17.4, ModDate 2026-09-15 Retrieved: 2026-10-22T12:05:00Z	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `f5d4fc4f3a65a2dc3ab696e165bb86bf150b2437cdc1a7046cfbecae8ccab05c` 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 Inspected artifact
Origin author_reported Context-only references	Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 Original source ↗ Supplementary Methods Table 6, row 'TcdB' (Designs screened = 96), column 'Success rate (%) (AF3)' Version: Supplementary Information PDF 41586_2025_9721_MOESM1_ESM.pdf, 129 pages, InDesign 17.4, ModDate 2026-09-15 Retrieved: 2026-10-22T12:05:00Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.origin` Source artifact SHA-256: `f5d4fc4f3a65a2dc3ab696e165bb86bf150b2437cdc1a7046cfbecae8ccab05c` 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 Inspected artifact

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record 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

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Technical metadata and extraction receipts

Stable ID: uc-binder-20261022-eval-bennett-tcdb-spr-insilico-af3-af3

areas: proteins-complexes; protein-structure
contexts: research
comparison: adaptation: AlphaFold3 filter; aggregation: Per target; budget: 200 backbones designed per target; dataset version: TcdB, Supplementary Methods Table 5 epitope; inputs: Cropped target structure with the Table 5 hotspot residues as the epitope; metric implementation: Share of designs passing the stated structural and confidence thresholds; population: 200 backbones per target, best of 8 ProteinMPNN sequences each; protocol id: uc-binder-20261022-protocol-bennett-insilico-af3-success; split: Not reported
missing metadata: comparison.split: note: A design campaign, not a train/test split.; reason: inapplicable
origin: author_reported
protocol: uc-binder-20261022-protocol-bennett-insilico-af3-success
retrospective: true
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 'TcdB' (Designs screened = 96), column 'Success rate (%) (AF3)'
version: Nature 2025 version of record; Supplementary Methods Table 6

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