Evidence claim

Relevance of uc-binder-20261022-protocol-alphaproteo-htrf-kd 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 best per-target binder affinity by HTRF
Relevance: Direct evidence
Endpoint: Lowest dissociation constant measured by HTRF among a target's expressed AlphaProteo or published-RFdiffusion yeast-display hits

The affinities reached are part of the endpoint this use case needs, and these are measured values with a stated assay. They answer 'how good is the best design' and not 'how many designs bind'.

25 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 Table 1, 'Binding KD (nM)' block; Table S2; Section S4.2 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: Table 1, 'Binding KD (nM)' block; Table S2; Section S4.2 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 binder-affinities 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: Table 1, 'Binding KD (nM)' block; Table S2; Section S4.2 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 Affinity of the best binder found per 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: Table 1, 'Binding KD (nM)' block; Table S2; Section S4.2 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 3 values A best-of-subset value. It describes the best design found among the hits that expressed, not the distribution of the designs. Do not compare HTRF values with BLI or SPR values. Section S4.2 reports that HTRF gave KD values about tenfold higher than published BLI values for two control binders. The AlphaProteo and RFdiffusion affinity evaluations are not a controlled comparison, for the same reason as the 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: Table 1, 'Binding KD (nM)' block; Table S2; Section S4.2 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 Lowest dissociation constant measured by HTRF among a target's expressed AlphaProteo or published-RFdiffusion yeast-display hits 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: Table 1, 'Binding KD (nM)' block; Table S2; Section S4.2 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-htrf-kd 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: Table 1, 'Binding KD (nM)' block; Table S2; Section S4.2 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 dissociation-constant 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: Table 1, 'Binding KD (nM)' block; Table S2; Section S4.2 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 4 values Developer-reported. Best-of-subset over a set the authors chose to follow up; no uncertainty is printed. The subset titrated is the yeast hits that expressed in E. coli, so the affinity carries the expression filter as well as the design and binding filters. 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: Table 1, 'Binding KD (nM)' block; Table S2; Section S4.2 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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uc-binder-20261022-result-alphaproteo-table1-rfdiffusion-kd-il7ra fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 8ced23031f0b29629afc936398eddc4a991e079cbe88bc067cdd4f93976539cc record id uc-binder-20261022-result-alphaproteo-table1-rfdiffusion-kd-pdl1 fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 cbb561d49401e7b52a0b77b39c93c9478eb4836f63381e5dc45186d95e2d45e8 record id uc-binder-20261022-result-alphaproteo-table1-rfdiffusion-kd-trka fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 3b436c82dbdb8c38a7300970d0baee10db27bab07db61a8d8a22cd8548b6b38a 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: Table 1, 'Binding KD (nM)' block; Table S2; Section S4.2 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 The affinities reached are part of the endpoint this use case needs, and these are measured values with a stated assay. They answer 'how good is the best design' and not 'how many designs bind'. 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: Table 1, 'Binding KD (nM)' block; Table S2; Section S4.2 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

How to read the evidence

Sources and history

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

1 source record and release history

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-htrf-kd

citation locators: locator: Table 1, 'Binding KD (nM)' block; Table S2; Section S4.2; source id: uc-binder-20261022-source-alphaproteo
comparison group: binder-affinities
comparison title: Affinity of the best binder found per target
constraints: A best-of-subset value. It describes the best design found among the hits that expressed, not the distribution of the designs.; Do not compare HTRF values with BLI or SPR values. Section S4.2 reports that HTRF gave KD values about tenfold higher than published BLI values for two control binders.; The AlphaProteo and RFdiffusion affinity evaluations are not a controlled comparison, for the same reason as the hit rates.
endpoint: Lowest dissociation constant measured by HTRF among a target's expressed AlphaProteo or published-RFdiffusion yeast-display hits
field: links:assessed_by:uc-binder-20261022-protocol-alphaproteo-htrf-kd
headline metric: dissociation-constant
limitations: Developer-reported.; Best-of-subset over a set the authors chose to follow up; no uncertainty is printed.; The subset titrated is the yeast hits that expressed in E. coli, so the affinity carries the expression filter as well as the design and binding filters.; Preprint, not peer reviewed.
rationale: The affinities reached are part of the endpoint this use case needs, and these are measured values with a stated assay. They answer 'how good is the best design' and not 'how many designs bind'.
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-kd-rfdiffusion-published-designs-il7ra-main; uc-binder-20261022-eval-alphaproteo-s2-kd-rfdiffusion-published-designs-pdl1-main; uc-binder-20261022-eval-alphaproteo-s2-kd-rfdiffusion-published-designs-trka-main; uc-binder-20261022-eval-alphaproteo-s2-kd-v1-bhrf1-main; uc-binder-20261022-eval-alphaproteo-s2-kd-v1-il17a-main; uc-binder-20261022-eval-alphaproteo-s2-kd-v1-il7ra-main; uc-binder-20261022-eval-alphaproteo-s2-kd-v1-improved-filter-pdl1-main; uc-binder-20261022-eval-alphaproteo-s2-kd-v1-improved-filter-sc2rbd-main; uc-binder-20261022-eval-alphaproteo-s2-kd-v1-pdl1-main; uc-binder-20261022-eval-alphaproteo-s2-kd-v1-sc2rbd-dagger; uc-binder-20261022-eval-alphaproteo-s2-kd-v1-sc2rbd-main; uc-binder-20261022-eval-alphaproteo-s2-kd-v1-trka-main; uc-binder-20261022-eval-alphaproteo-s2-kd-v1-vegfa-main; uc-binder-20261022-eval-alphaproteo-s2-kd-v2-pdl1-main; uc-binder-20261022-eval-alphaproteo-s2-kd-v2-trka-main; uc-binder-20261022-eval-alphaproteo-table1-kd-bhrf1; uc-binder-20261022-eval-alphaproteo-table1-kd-il17a; uc-binder-20261022-eval-alphaproteo-table1-kd-il7ra; uc-binder-20261022-eval-alphaproteo-table1-kd-pdl1; uc-binder-20261022-eval-alphaproteo-table1-kd-sc2rbd; uc-binder-20261022-eval-alphaproteo-table1-kd-trka; uc-binder-20261022-eval-alphaproteo-table1-kd-vegfa; uc-binder-20261022-eval-alphaproteo-table1-rfdiffusion-kd-il7ra; uc-binder-20261022-eval-alphaproteo-table1-rfdiffusion-kd-pdl1; uc-binder-20261022-eval-alphaproteo-table1-rfdiffusion-kd-trka
revision: 1
source locator: uc-binder-20261022-source-alphaproteo: Table 1, 'Binding KD (nM)' block; Table S2; Section S4.2
stratum label: AlphaProteo and published RFdiffusion designs, HTRF
stratum order: 1
value: uc-binder-20261022-protocol-alphaproteo-htrf-kd
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