Evidence claim

Relevance of uc-binder-20261022-protocol-bennett-insilico-rf2-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 the fine-tuned RoseTTAFold2 filter
Relevance: outside_scope
Endpoint: Share of designed antibody variable heavy chains that pass a fine-tuned RoseTTAFold2 filter, at three proportions of interface hotspots provided

Outside the use case's endpoint. This is a computational filter pass rate, which the issue defines as a step inside the pipeline rather than an outcome. It is kept because it quantifies the filter that chose the tested designs, and because the table caption gives its purpose as estimating compute requirements, not as evidence about binders.

18 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 statement	Original source and location	Review and provenance
Citation locations 1 values locator Supplementary Methods Table 6, columns 'Success rate (%) (RF2, hotspot proportion = 1 / 0.1 / 0.0)' 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, columns 'Success rate (%) (RF2, hotspot proportion = 1 / 0.1 / 0.0)' 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, columns 'Success rate (%) (RF2, hotspot proportion = 1 / 0.1 / 0.0)' 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, columns 'Success rate (%) (RF2, hotspot proportion = 1 / 0.1 / 0.0)' 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 2 values Not an outcome. Do not present these values alongside measured hit rates. Use them only to describe how the tested set was chosen and how much compute a design library costs. 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, columns 'Success rate (%) (RF2, hotspot proportion = 1 / 0.1 / 0.0)' 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 a fine-tuned RoseTTAFold2 filter, at three proportions of interface hotspots provided 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, columns 'Success rate (%) (RF2, hotspot proportion = 1 / 0.1 / 0.0)' 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-rf2-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, columns 'Success rate (%) (RF2, hotspot proportion = 1 / 0.1 / 0.0)' 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, columns 'Success rate (%) (RF2, hotspot proportion = 1 / 0.1 / 0.0)' 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 4 values An in silico filter pass rate, not a measured outcome. The filter is the authors' own, and the caption states that the setting used for filtering in the work 'is likely not the most predictive setting'. The H1 stem 9,000-design row repeats the 96-design row's values in parentheses, because both come from one design campaign. 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, columns 'Success rate (%) (RF2, hotspot proportion = 1 / 0.1 / 0.0)' 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
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sha256 b5a0012d1b0f02d6bd7466b7308123b26e676eda8ef54d706c865bb3f777e5b9 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, columns 'Success rate (%) (RF2, hotspot proportion = 1 / 0.1 / 0.0)' 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. This is a computational filter pass rate, which the issue defines as a step inside the pipeline rather than an outcome. It is kept because it quantifies the filter that chose the tested designs, and because the table caption gives its purpose as estimating compute requirements, not as evidence about binders. 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, columns 'Success rate (%) (RF2, hotspot proportion = 1 / 0.1 / 0.0)' 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

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

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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: use-case-mapping-binder-20261022-bennett-insilico-rf2-success

citation locators: locator: Supplementary Methods Table 6, columns 'Success rate (%) (RF2, hotspot proportion = 1 / 0.1 / 0.0)'; 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. Do not present these values alongside measured hit rates.; Use them only to describe how the tested set was chosen and how much compute a design library costs.
endpoint: Share of designed antibody variable heavy chains that pass a fine-tuned RoseTTAFold2 filter, at three proportions of interface hotspots provided
field: links:assessed_by:uc-binder-20261022-protocol-bennett-insilico-rf2-success
headline metric: success-rate
limitations: An in silico filter pass rate, not a measured outcome.; The filter is the authors' own, and the caption states that the setting used for filtering in the work 'is likely not the most predictive setting'.; The H1 stem 9,000-design row repeats the 96-design row's values in parentheses, because both come from one design campaign.; No uncertainty is printed.
rationale: Outside the use case's endpoint. This is a computational filter pass rate, which the issue defines as a step inside the pipeline rather than an outcome. It is kept because it quantifies the filter that chose the tested designs, and because the table caption gives its purpose as estimating compute requirements, not as evidence about binders.
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-rf2-0-0; uc-binder-20261022-eval-bennett-h1stem-spr-insilico-rf2-0-1; uc-binder-20261022-eval-bennett-h1stem-spr-insilico-rf2-1; uc-binder-20261022-eval-bennett-h1stem-ysd-insilico-rf2-0-0; uc-binder-20261022-eval-bennett-h1stem-ysd-insilico-rf2-0-1; uc-binder-20261022-eval-bennett-h1stem-ysd-insilico-rf2-1; uc-binder-20261022-eval-bennett-il7r-spr-insilico-rf2-0-0; uc-binder-20261022-eval-bennett-il7r-spr-insilico-rf2-0-1; uc-binder-20261022-eval-bennett-il7r-spr-insilico-rf2-1; uc-binder-20261022-eval-bennett-rbd-ysd-insilico-rf2-0-0; uc-binder-20261022-eval-bennett-rbd-ysd-insilico-rf2-0-1; uc-binder-20261022-eval-bennett-rbd-ysd-insilico-rf2-1; uc-binder-20261022-eval-bennett-rsv3-ysd-insilico-rf2-0-0; uc-binder-20261022-eval-bennett-rsv3-ysd-insilico-rf2-0-1; uc-binder-20261022-eval-bennett-rsv3-ysd-insilico-rf2-1; uc-binder-20261022-eval-bennett-tcdb-spr-insilico-rf2-0-0; uc-binder-20261022-eval-bennett-tcdb-spr-insilico-rf2-0-1; uc-binder-20261022-eval-bennett-tcdb-spr-insilico-rf2-1
revision: 1
source locator: uc-binder-20261022-source-bennett-si: Supplementary Methods Table 6, columns 'Success rate (%) (RF2, hotspot proportion = 1 / 0.1 / 0.0)'
stratum label: Fine-tuned RoseTTAFold2 filter pass rates
stratum order: 1
value: uc-binder-20261022-protocol-bennett-insilico-rf2-success
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