Evidence claim

Relevance of uc-binder-20261022-protocol-alphaproteo-yeast-display-signal-0-2 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: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2
Relevance: Direct evidence
Endpoint: Share of tested AlphaProteo or published-RFdiffusion designs whose yeast-display binding signal exceeds 0.2, per target, with the number of designs tested

A measured wet-lab binding outcome on seven targets, with the design denominator printed for every value. It is the only source found where two design methods were measured on the same assay for the same targets, so it carries the most weight any single source here can. It is not a controlled comparison: the AlphaProteo authors ran the assay, and Section S4.1 states that the RFdiffusion arm is the published RFdiffusion designs re-tested rather than RFdiffusion as run by them.

26 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 Section S1.2.1; Table 1; Table S2 source id uc-binder-20261022-source-alphaproteo Context-only references	De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) Original source ↗ uc-binder-20261022-source-alphaproteo: Section S1.2.1; Table 1; Table S2 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) Retrieved: 2026-10-22T11:53:00Z	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: `953b35644c0fa06ff090d7614c2e19525831f8fde50242e176d54474133c5a42` Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. Inspected artifact
Comparison group miniprotein-binder-hit-rates Context-only references	De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) Original source ↗ uc-binder-20261022-source-alphaproteo: Section S1.2.1; Table 1; Table S2 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) Retrieved: 2026-10-22T11:53:00Z	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: `953b35644c0fa06ff090d7614c2e19525831f8fde50242e176d54474133c5a42` Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. Inspected artifact
Comparison title Miniprotein binder hit rates by target Context-only references	De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) Original source ↗ uc-binder-20261022-source-alphaproteo: Section S1.2.1; Table 1; Table S2 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) Retrieved: 2026-10-22T11:53:00Z	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: `953b35644c0fa06ff090d7614c2e19525831f8fde50242e176d54474133c5a42` Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. Inspected artifact
Constraints 4 values Do not read the AlphaProteo and RFdiffusion evaluations on a target as a controlled comparison. The assay is shared; the design and selection steps are not, and the evaluations' selection, population and budget comparison fields are null for that reason. Do not compare these rates with the BLI, SPR or display rates in any other protocol. A binding signal above 0.2 on this instrument is not the same endpoint as a fitted affinity threshold. Read each value with its printed denominator. They range from 30 to 172 designs. Table 1's AlphaProteo values pool up to three different design systems; the Table S2 evaluations separate them and are the better evidence for what one system achieves. Context-only references	De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) Original source ↗ uc-binder-20261022-source-alphaproteo: Section S1.2.1; Table 1; Table S2 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) Retrieved: 2026-10-22T11:53:00Z	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: `953b35644c0fa06ff090d7614c2e19525831f8fde50242e176d54474133c5a42` Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. Inspected artifact
Endpoint Share of tested AlphaProteo or published-RFdiffusion designs whose yeast-display binding signal exceeds 0.2, per target, with the number of designs tested Context-only references	De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) Original source ↗ uc-binder-20261022-source-alphaproteo: Section S1.2.1; Table 1; Table S2 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) Retrieved: 2026-10-22T11:53:00Z	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: `953b35644c0fa06ff090d7614c2e19525831f8fde50242e176d54474133c5a42` Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. Inspected artifact
Claimed field links:assessed_by:uc-binder-20261022-protocol-alphaproteo-yeast-display-signal-0-2 Context-only references	De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) Original source ↗ uc-binder-20261022-source-alphaproteo: Section S1.2.1; Table 1; Table S2 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) Retrieved: 2026-10-22T11:53:00Z	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: `953b35644c0fa06ff090d7614c2e19525831f8fde50242e176d54474133c5a42` Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. Inspected artifact
Headline metric hit-rate Context-only references	De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) Original source ↗ uc-binder-20261022-source-alphaproteo: Section S1.2.1; Table 1; Table S2 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) Retrieved: 2026-10-22T11:53:00Z	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: `953b35644c0fa06ff090d7614c2e19525831f8fde50242e176d54474133c5a42` Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. Inspected artifact
Limitations 6 values Developer-reported: the authors built AlphaProteo, chose the targets, ran the assay and chose which designs to test with their own filter. The hit threshold was calibrated manually by visual inspection of raw scatterplots. No conventional comparator was run on these targets. No uncertainty is printed for any rate. Target concentrations were 10- to 20-fold lower than in the RFdiffusion publication, which the authors say 'may exclude lower-affinity hits'. Preprint, not peer reviewed. Context-only references	De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) Original source ↗ uc-binder-20261022-source-alphaproteo: Section S1.2.1; Table 1; Table S2 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) Retrieved: 2026-10-22T11:53:00Z	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: `953b35644c0fa06ff090d7614c2e19525831f8fde50242e176d54474133c5a42` Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. Inspected artifact
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status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 4dd588ce093e118a7d023d6325a2d52048b99c56967c6235255a8caabe5ce5e0 record id uc-binder-20261022-result-alphaproteo-table1-rfdiffusion-hitrate-trka fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 80fb64abe50f2dd8bfab5215fed78747ae6fa70675a78abe481338ed18c5764f record id uc-binder-20261022-source-alphaproteo fields status attributes.artifact_sha256 sha256 4f4d69e2483d41e1016f2b3c6f078632280b3ca9ada6ac9f76e5ad7c16c914a0 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	De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) Original source ↗ uc-binder-20261022-source-alphaproteo: Section S1.2.1; Table 1; Table S2 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) Retrieved: 2026-10-22T11:53:00Z	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: `953b35644c0fa06ff090d7614c2e19525831f8fde50242e176d54474133c5a42` Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. Inspected artifact
Rationale A measured wet-lab binding outcome on seven targets, with the design denominator printed for every value. It is the only source found where two design methods were measured on the same assay for the same targets, so it carries the most weight any single source here can. It is not a controlled comparison: the AlphaProteo authors ran the assay, and Section S4.1 states that the RFdiffusion arm is the published RFdiffusion designs re-tested rather than RFdiffusion as run by them. Context-only references	De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) Original source ↗ uc-binder-20261022-source-alphaproteo: Section S1.2.1; Table 1; Table S2 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) Retrieved: 2026-10-22T11:53:00Z	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: `953b35644c0fa06ff090d7614c2e19525831f8fde50242e176d54474133c5a42` Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. Inspected artifact

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Sources and history

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

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De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Original source · arXiv version 1, posted 2024-09-12; full-text PDF (49 pages)

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-binder-20261022-alphaproteo-yeast-display-signal-0-2

citation locators: locator: Section S1.2.1; Table 1; Table S2; source id: uc-binder-20261022-source-alphaproteo
comparison group: miniprotein-binder-hit-rates
comparison title: Miniprotein binder hit rates by target
constraints: Do not read the AlphaProteo and RFdiffusion evaluations on a target as a controlled comparison. The assay is shared; the design and selection steps are not, and the evaluations' selection, population and budget comparison fields are null for that reason.; Do not compare these rates with the BLI, SPR or display rates in any other protocol. A binding signal above 0.2 on this instrument is not the same endpoint as a fitted affinity threshold.; Read each value with its printed denominator. They range from 30 to 172 designs.; Table 1's AlphaProteo values pool up to three different design systems; the Table S2 evaluations separate them and are the better evidence for what one system achieves.
endpoint: Share of tested AlphaProteo or published-RFdiffusion designs whose yeast-display binding signal exceeds 0.2, per target, with the number of designs tested
field: links:assessed_by:uc-binder-20261022-protocol-alphaproteo-yeast-display-signal-0-2
headline metric: hit-rate
limitations: Developer-reported: the authors built AlphaProteo, chose the targets, ran the assay and chose which designs to test with their own filter.; The hit threshold was calibrated manually by visual inspection of raw scatterplots.; No conventional comparator was run on these targets.; No uncertainty is printed for any rate.; Target concentrations were 10- to 20-fold lower than in the RFdiffusion publication, which the authors say 'may exclude lower-affinity hits'.; Preprint, not peer reviewed.
rationale: A measured wet-lab binding outcome on seven targets, with the design denominator printed for every value. It is the only source found where two design methods were measured on the same assay for the same targets, so it carries the most weight any single source here can. It is not a controlled comparison: the AlphaProteo authors ran the assay, and Section S4.1 states that the RFdiffusion arm is the published RFdiffusion designs re-tested rather than RFdiffusion as run by them.
reason: Add measured de novo binder design outcomes from the 2026-10-22 use-case evidence pass (#176).
relevance: direct
review: artifact sha256: 953b35644c0fa06ff090d7614c2e19525831f8fde50242e176d54474133c5a42; method: scope-review; independent-cell-check; ai-assisted-source-review; method note: Re-downloaded with curl (HTTP 200, 12,333,400 bytes) and the SHA-256 recomputed and matched. Own text layer made with pdftotext -layout (poppler 26.08.0), reproducing the extraction pass's 2,811 lines. Table 1, Table S2, Table S3 and Sections S1.2.1, S2, S4.1 and S4.2 read cell by cell and compared with every record. Column assignment re-derived arithmetically rather than trusted.; 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://arxiv.org/pdf/2409.08022v1; 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-alphaproteo-s2-rate-rfdiffusion-published-designs-il7ra-main; uc-binder-20261022-eval-alphaproteo-s2-rate-rfdiffusion-published-designs-pdl1-main; uc-binder-20261022-eval-alphaproteo-s2-rate-rfdiffusion-published-designs-trka-main; uc-binder-20261022-eval-alphaproteo-s2-rate-v1-bhrf1-main; uc-binder-20261022-eval-alphaproteo-s2-rate-v1-il7ra-main; uc-binder-20261022-eval-alphaproteo-s2-rate-v1-improved-filter-pdl1-main; uc-binder-20261022-eval-alphaproteo-s2-rate-v1-improved-filter-sc2rbd-main; uc-binder-20261022-eval-alphaproteo-s2-rate-v1-pdl1-main; uc-binder-20261022-eval-alphaproteo-s2-rate-v1-sc2rbd-dagger; uc-binder-20261022-eval-alphaproteo-s2-rate-v1-sc2rbd-main; uc-binder-20261022-eval-alphaproteo-s2-rate-v1-tnfa-main; uc-binder-20261022-eval-alphaproteo-s2-rate-v1-trka-main; uc-binder-20261022-eval-alphaproteo-s2-rate-v1-vegfa-main; uc-binder-20261022-eval-alphaproteo-s2-rate-v2-pdl1-main; uc-binder-20261022-eval-alphaproteo-s2-rate-v2-tnfa-main; uc-binder-20261022-eval-alphaproteo-s2-rate-v2-trka-main; uc-binder-20261022-eval-alphaproteo-table1-rate-bhrf1; uc-binder-20261022-eval-alphaproteo-table1-rate-il7ra; uc-binder-20261022-eval-alphaproteo-table1-rate-pdl1; uc-binder-20261022-eval-alphaproteo-table1-rate-sc2rbd; uc-binder-20261022-eval-alphaproteo-table1-rate-tnfa; uc-binder-20261022-eval-alphaproteo-table1-rate-trka; uc-binder-20261022-eval-alphaproteo-table1-rate-vegfa; uc-binder-20261022-eval-alphaproteo-table1-rfdiffusion-rate-il7ra; uc-binder-20261022-eval-alphaproteo-table1-rfdiffusion-rate-pdl1; uc-binder-20261022-eval-alphaproteo-table1-rfdiffusion-rate-trka
revision: 1
source locator: uc-binder-20261022-source-alphaproteo: Section S1.2.1; Table 1; Table S2
stratum label: AlphaProteo and published RFdiffusion designs, yeast display at signal above 0.2
stratum order: 1
value: uc-binder-20261022-protocol-alphaproteo-yeast-display-signal-0-2
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