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Evidence claim

Relevance of uc-binder-20261022-protocol-bennett-insilico-af3-success 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 computational success rate under an AlphaFold3 filter
Relevance
outside_scope
Endpoint
Share of designed antibody variable heavy chains that pass an AlphaFold3 filter at Ca RMSD below 5 A and ipTM above 0.5

Outside the use case's endpoint, and retrospective: AlphaFold3 was released after the design work. Kept because the paper uses it to argue that a better filter would raise the measured success rate, which is a claim about the selection step that the use case has to keep separate from the design step.

6 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.

20 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statementOriginal source and locationReview and provenance
Citation locations
1 values
  • locator
    Supplementary Methods Table 6, column 'Success rate (%) (AF3)'
    source id
    uc-binder-20261022-source-bennett-si
Context-only references		Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6

Original source ↗

uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, 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

Audit details

Field: attributes.citation_locators

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 group
in-silico-filters
Context-only references		Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6

Original source ↗

uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, 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

Audit details

Field: attributes.comparison_group

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 title
Computational filters used to choose which designs to test
Context-only references		Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6

Original source ↗

uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, 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

Audit details

Field: attributes.comparison_title

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

Constraints
3 values
  • Not an outcome, and retrospective.
  • The values are depressed by AlphaFold3 re-predicting the cropped design targets inaccurately, which the caption states explicitly.
  • Do not read a low AlphaFold3 pass rate as evidence about the designs.
Context-only references		Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6

Original source ↗

uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, 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

Audit details

Field: attributes.constraints

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

Endpoint
Share of designed antibody variable heavy chains that pass an AlphaFold3 filter at Ca RMSD below 5 A and ipTM above 0.5
Context-only references		Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6

Original source ↗

uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, 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

Audit details

Field: attributes.endpoint

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

Claimed field
links:assessed_by:uc-binder-20261022-protocol-bennett-insilico-af3-success
Context-only references		Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6

Original source ↗

uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, 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

Audit details

Field: attributes.field

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

Headline metric
success-rate
Context-only references		Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6

Original source ↗

uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, 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

Audit details

Field: attributes.headline_metric

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

Limitations
5 values
  • An in silico filter pass rate, not a measured outcome.
  • Retrospective: the filter was not available when the designs were made.
  • The caption states that cropped targets were not accurately re-predicted and that 'success rates would likely be higher with contiguous (non-cropped) targets'.
  • The RSV site 3 value carries an asterisk recording a 19 A target-epitope prediction error.
  • No uncertainty is printed.
Context-only references		Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6

Original source ↗

uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, 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

Audit details

Field: attributes.limitations

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

Pinned records
16 values
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Context-only references		Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6

Original source ↗

uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, 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

Audit details

Field: attributes.pins

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

Rationale
Outside the use case's endpoint, and retrospective: AlphaFold3 was released after the design work. Kept because the paper uses it to argue that a better filter would raise the measured success rate, which is a claim about the selection step that the use case has to keep separate from the design step.
Context-only references		Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6

Original source ↗

uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, 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

Audit details

Field: attributes.rationale

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

How to read the evidence

Sources and history

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

1 source record and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: use-case-mapping-binder-20261022-bennett-insilico-af3-success

citation locators
locator: Supplementary Methods Table 6, column 'Success rate (%) (AF3)'; source id: uc-binder-20261022-source-bennett-si
comparison group
in-silico-filters
comparison title
Computational filters used to choose which designs to test
constraints
Not an outcome, and retrospective.; The values are depressed by AlphaFold3 re-predicting the cropped design targets inaccurately, which the caption states explicitly.; Do not read a low AlphaFold3 pass rate as evidence about the designs.
endpoint
Share of designed antibody variable heavy chains that pass an AlphaFold3 filter at Ca RMSD below 5 A and ipTM above 0.5
field
links:assessed_by:uc-binder-20261022-protocol-bennett-insilico-af3-success
headline metric
success-rate
limitations
An in silico filter pass rate, not a measured outcome.; Retrospective: the filter was not available when the designs were made.; The caption states that cropped targets were not accurately re-predicted and that 'success rates would likely be higher with contiguous (non-cropped) targets'.; The RSV site 3 value carries an asterisk recording a 19 A target-epitope prediction error.; No uncertainty is printed.
rationale
Outside the use case's endpoint, and retrospective: AlphaFold3 was released after the design work. Kept because the paper uses it to argue that a better filter would raise the measured success rate, which is a claim about the selection step that the use case has to keep separate from the design step.
reason
Add measured de novo binder design outcomes from the 2026-10-22 use-case evidence pass (#176).
relevance
outside_scope
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-insilico-af3-af3; uc-binder-20261022-eval-bennett-h1stem-ysd-insilico-af3-af3; uc-binder-20261022-eval-bennett-il7r-spr-insilico-af3-af3; uc-binder-20261022-eval-bennett-rbd-ysd-insilico-af3-af3; uc-binder-20261022-eval-bennett-rsv3-ysd-insilico-af3-af3; uc-binder-20261022-eval-bennett-tcdb-spr-insilico-af3-af3
revision
1
source locator
uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, column 'Success rate (%) (AF3)'
stratum label
AlphaFold3 filter pass rates
stratum order
2
value
uc-binder-20261022-protocol-bennett-insilico-af3-success
pins
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