Evidence claim

Relevance of uc-binder-20261022-protocol-bindcraft-mean-success-rate-12-targets to "Which computational design workflow produces binders that work when they are made and tested?"

Evidence concern: excluded from comparisons

Supplementary Data 1 has one row per tested design with a Binding column holding 1, 0 or an empty cell. Treating the non-empty cells as the tested set reproduces the prose counts for BBF-14 (11 tested, 6 binding), Bet v1 (7, 2), CD45 (16, 4), Der f7 (10, 4), Der f21 (7, 4), IFNAR2 (9, 3), PD-1 (53, 13), SpCas9 (6, 6) and CLDN1 (7, 6), but not for PD-L1 (13 non-empty rows with 11 binding against 9 tested with 7 binding in the prose), CrSAS-6 (10 non-empty rows against 9 tested) or CbAgo (2 non-empty rows against 12 tested). The row filter is therefore ambiguous and no value is computed from these rows.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Results prose; Fig. 1b caption

Fig. 1b's caption defines success as binding observed on SPR, but the PD-1 screen was BLI in a bivalent Fc-fusion format and the CLDN1 screen used soluble analogues. The 46.3% average therefore pools targets measured under different endpoints.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Fig. 1b caption; Results 'Binders targeting cell-surface receptors' and 'Targeting unexplored binding sites'

Use case: Design a new binder to a chosen target
Assessed by: BindCraft experimental success rate averaged over its 12 benchmark targets
Relevance: Direct evidence
Endpoint: Mean and range of BindCraft's per-target experimental success rate over its 12 benchmark targets

The headline claim this use case has to adjudicate, recorded with what it actually is: an unweighted mean over twelve author-chosen targets whose denominators range from 6 to 53 designs, spanning rates from 10% to 100%. The range is the finding, not the mean.

1 reviewed evaluation

BindCraft experimental success rate over its 12 benchmark targets

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

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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 Introduction, final paragraph source id uc-binder-20261022-source-bindcraft Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ uc-binder-20261022-source-bindcraft: Introduction, final paragraph Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group miniprotein-binder-hit-rates Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ uc-binder-20261022-source-bindcraft: Introduction, final paragraph Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Miniprotein binder hit rates by target Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ uc-binder-20261022-source-bindcraft: Introduction, final paragraph Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 3 values The mean is unweighted over targets, not pooled over designs. A target where 6 of 6 designs bound contributes as much as one where 13 of 53 did. Do not compare this mean with any single-target rate in another protocol. The 10% to 100% range belongs with the mean whenever the mean is cited. Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ uc-binder-20261022-source-bindcraft: Introduction, final paragraph Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.constraints` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint Mean and range of BindCraft's per-target experimental success rate over its 12 benchmark targets Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ uc-binder-20261022-source-bindcraft: Introduction, final paragraph Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.endpoint` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field links:assessed_by:uc-binder-20261022-protocol-bindcraft-mean-success-rate-12-targets Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ uc-binder-20261022-source-bindcraft: Introduction, final paragraph Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.field` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Headline metric hit-rate Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ uc-binder-20261022-source-bindcraft: Introduction, final paragraph Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.headline_metric` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Limitations 4 values Developer-reported, with author-chosen targets. Pools targets measured under different endpoints: SPR, a bivalent-Fc BLI screen, and a soluble analogue prescreen. Two of the twelve per-target numerators were not read, so the mean cannot be checked against the per-target counts in this batch. No conventional comparator. No uncertainty is printed. Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ uc-binder-20261022-source-bindcraft: Introduction, final paragraph Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.limitations` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Pinned records 6 values record id uc-binder-20261022-eval-bindcraft-aggregate-12-targets fields status links attributes.origin attributes.comparison sha256 6332d6bc9001923d9308a867c4272aea4c037c509c69703aa600a013fcbf6b9c record id uc-binder-20261022-protocol-bindcraft-mean-success-rate-12-targets fields status name description facets source_ids links attributes sha256 486d4821b502112421458f244e4f31dbfbec6403c43d1ab620fd5103bf2d0a16 record id uc-binder-20261022-result-bindcraft-mean-success-rate fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 6ce04d323102f3f7272b19761b82b2beba611a19086442990fd9705442eb8621 record id uc-binder-20261022-result-bindcraft-success-rate-range fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 75fe499e5396202772addf5da7cbc5b8f65d4845b19fa6e8f7c7f8e1d90d3272 record id uc-binder-20261022-source-bindcraft fields status attributes.artifact_sha256 sha256 d3bd9c67fe1a3b209916f330437cb5ff046ad76c4666c0976e40a65549ba279f 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 Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ uc-binder-20261022-source-bindcraft: Introduction, final paragraph Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.pins` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Rationale The headline claim this use case has to adjudicate, recorded with what it actually is: an unweighted mean over twelve author-chosen targets whose denominators range from 6 to 53 designs, spanning rates from 10% to 100%. The range is the finding, not the mean. Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ uc-binder-20261022-source-bindcraft: Introduction, final paragraph Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.rationale` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

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

1 source record and release history

One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Original source · Nature, version of record; Europe PMC JATS full text for PMC12507698

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-binder-20261022-bindcraft-mean-success-rate-12-targets

citation locators: locator: Introduction, final paragraph; source id: uc-binder-20261022-source-bindcraft
comparison group: miniprotein-binder-hit-rates
comparison title: Miniprotein binder hit rates by target
constraints: The mean is unweighted over targets, not pooled over designs. A target where 6 of 6 designs bound contributes as much as one where 13 of 53 did.; Do not compare this mean with any single-target rate in another protocol.; The 10% to 100% range belongs with the mean whenever the mean is cited.
endpoint: Mean and range of BindCraft's per-target experimental success rate over its 12 benchmark targets
field: links:assessed_by:uc-binder-20261022-protocol-bindcraft-mean-success-rate-12-targets
headline metric: hit-rate
limitations: Developer-reported, with author-chosen targets.; Pools targets measured under different endpoints: SPR, a bivalent-Fc BLI screen, and a soluble analogue prescreen.; Two of the twelve per-target numerators were not read, so the mean cannot be checked against the per-target counts in this batch.; No conventional comparator. No uncertainty is printed.
rationale: The headline claim this use case has to adjudicate, recorded with what it actually is: an unweighted mean over twelve author-chosen targets whose denominators range from 6 to 53 designs, spanning rates from 10% to 100%. The range is the finding, not the mean.
reason: Add measured de novo binder design outcomes from the 2026-10-22 use-case evidence pass (#176).
relevance: direct
review: artifact sha256: 74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d; method: scope-review; independent-cell-check; ai-assisted-source-review; method note: Re-downloaded from Europe PMC (HTTP 200, 226,059 bytes) and the SHA-256 recomputed and matched. Own flattening of the JATS XML; every quoted locator sentence and every printed value checked verbatim against it by a parser written for this review.; 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/PMC12507698/fullTextXML; 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-bindcraft-aggregate-12-targets
revision: 1
source locator: uc-binder-20261022-source-bindcraft: Introduction, final paragraph
stratum label: BindCraft average over 12 targets
stratum order: 4
value: uc-binder-20261022-protocol-bindcraft-mean-success-rate-12-targets
pins: record id: uc-binder-20261022-eval-bindcraft-aggregate-12-targets; fields: status; links; attributes.origin; attributes.comparison; sha256: 6332d6bc9001923d9308a867c4272aea4c037c509c69703aa600a013fcbf6b9c; record id: uc-binder-20261022-protocol-bindcraft-mean-success-rate-12-targets; fields: status; name; description; facets; source_ids; links; attributes; sha256: 486d4821b502112421458f244e4f31dbfbec6403c43d1ab620fd5103bf2d0a16; record id: uc-binder-20261022-result-bindcraft-mean-success-rate; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 6ce04d323102f3f7272b19761b82b2beba611a19086442990fd9705442eb8621; record id: uc-binder-20261022-result-bindcraft-success-rate-range; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 75fe499e5396202772addf5da7cbc5b8f65d4845b19fa6e8f7c7f8e1d90d3272; record id: uc-binder-20261022-source-bindcraft; fields: status; attributes.artifact_sha256; sha256: d3bd9c67fe1a3b209916f330437cb5ff046ad76c4666c0976e40a65549ba279f; 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

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subject: Design a new binder to a chosen target

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