Evidence claim
Relevance of uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel 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 expression and HTRF confirmation funnel for yeast-display hits
- Relevance
- Proxy evidence
- Endpoint
- Counts of AlphaProteo yeast-display hits that were selected for E. coli expression, subcloned and expressed, tested by HTRF, and showed HTRF binding, per target
Proxy evidence. The issue asks for the filtering funnel to be recorded, and this is the only source that prints it stage by stage. It measures attrition between a display hit and a confirmed, expressible binder, which is not the binding endpoint itself but is what determines how much work a hit rate actually buys.
28 reviewed evaluations
- AlphaProteo observed htrf binding for BHRF1 (Table S3)
- AlphaProteo observed htrf binding for IL-17A (Table S3)
- AlphaProteo observed htrf binding for IL-7RA (Table S3)
- AlphaProteo observed htrf binding for PD-L1 (Table S3)
- AlphaProteo observed htrf binding for SC2RBD (Table S3)
- AlphaProteo observed htrf binding for TrkA (Table S3)
- AlphaProteo observed htrf binding for VEGF-A (Table S3)
- AlphaProteo successfully subcloned and expressed for BHRF1 (Table S3)
- AlphaProteo successfully subcloned and expressed for IL-17A (Table S3)
- AlphaProteo successfully subcloned and expressed for IL-7RA (Table S3)
- AlphaProteo successfully subcloned and expressed for PD-L1 (Table S3)
- AlphaProteo successfully subcloned and expressed for SC2RBD (Table S3)
- AlphaProteo successfully subcloned and expressed for TrkA (Table S3)
- AlphaProteo successfully subcloned and expressed for VEGF-A (Table S3)
- AlphaProteo tested by htrf for BHRF1 (Table S3)
- AlphaProteo tested by htrf for IL-17A (Table S3)
- AlphaProteo tested by htrf for IL-7RA (Table S3)
- AlphaProteo tested by htrf for PD-L1 (Table S3)
- AlphaProteo tested by htrf for SC2RBD (Table S3)
- AlphaProteo tested by htrf for TrkA (Table S3)
- AlphaProteo tested by htrf for VEGF-A (Table S3)
- AlphaProteo yeast surface display hits selected for e. coli expression for BHRF1 (Table S3)
- AlphaProteo yeast surface display hits selected for e. coli expression for IL-17A (Table S3)
- AlphaProteo yeast surface display hits selected for e. coli expression for IL-7RA (Table S3)
- AlphaProteo yeast surface display hits selected for e. coli expression for PD-L1 (Table S3)
- AlphaProteo yeast surface display hits selected for e. coli expression for SC2RBD (Table S3)
- AlphaProteo yeast surface display hits selected for e. coli expression for TrkA (Table S3)
- AlphaProteo yeast surface display hits selected for e. coli expression for VEGF-A (Table S3)
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
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Citation locations1 values
| De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) uc-binder-20261022-source-alphaproteo: Table S3 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. |
| Comparison group pipeline-attrition Context-only references | De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) uc-binder-20261022-source-alphaproteo: Table S3 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. |
| Comparison title Attrition between a screen hit and a confirmed binder Context-only references | De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) uc-binder-20261022-source-alphaproteo: Table S3 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. |
Constraints2 values
| De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) uc-binder-20261022-source-alphaproteo: Table S3 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. |
| Endpoint Counts of AlphaProteo yeast-display hits that were selected for E. coli expression, subcloned and expressed, tested by HTRF, and showed HTRF binding, per target Context-only references | De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) uc-binder-20261022-source-alphaproteo: Table S3 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. |
| Claimed field links:assessed_by:uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Context-only references | De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) uc-binder-20261022-source-alphaproteo: Table S3 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. |
| Headline metric count Context-only references | De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) uc-binder-20261022-source-alphaproteo: Table S3 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. |
Limitations4 values
| De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) uc-binder-20261022-source-alphaproteo: Table S3 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. |
Pinned records59 values
| De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) uc-binder-20261022-source-alphaproteo: Table S3 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. |
| Rationale Proxy evidence. The issue asks for the filtering funnel to be recorded, and this is the only source that prints it stage by stage. It measures attrition between a display hit and a confirmed, expressible binder, which is not the binding endpoint itself but is what determines how much work a hit rate actually buys. Context-only references | De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) uc-binder-20261022-source-alphaproteo: Table S3 Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. |
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)
Technical metadata and extraction receipts
Stable ID: use-case-mapping-binder-20261022-alphaproteo-ecoli-htrf-funnel
- citation locators
- locator: Table S3; source id: uc-binder-20261022-source-alphaproteo
- comparison group
- pipeline-attrition
- comparison title
- Attrition between a screen hit and a confirmed binder
- constraints
- These are counts of designs surviving a stage, not a hit rate. The first stage's denominator is an author choice and is not printed.; Do not use these counts to recompute the hit rates: the number of yeast hits available to select from is not stated.
- endpoint
- Counts of AlphaProteo yeast-display hits that were selected for E. coli expression, subcloned and expressed, tested by HTRF, and showed HTRF binding, per target
- field
- links:assessed_by:uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel
- headline metric
- count
- limitations
- Developer-reported.; The number of yeast hits selected for follow-up is an author choice, not the full hit set, so the funnel cannot be closed back to the screen.; TNF-alpha has no column, consistent with its 0% hit rate; its absence is not a recorded zero.; Preprint, not peer reviewed.
- rationale
- Proxy evidence. The issue asks for the filtering funnel to be recorded, and this is the only source that prints it stage by stage. It measures attrition between a display hit and a confirmed, expressible binder, which is not the binding endpoint itself but is what determines how much work a hit rate actually buys.
- reason
- Add measured de novo binder design outcomes from the 2026-10-22 use-case evidence pass (#176).
- relevance
- proxy
- 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-s3-observed-htrf-binding-bhrf1; uc-binder-20261022-eval-alphaproteo-s3-observed-htrf-binding-il17a; uc-binder-20261022-eval-alphaproteo-s3-observed-htrf-binding-il7ra; uc-binder-20261022-eval-alphaproteo-s3-observed-htrf-binding-pdl1; uc-binder-20261022-eval-alphaproteo-s3-observed-htrf-binding-sc2rbd; uc-binder-20261022-eval-alphaproteo-s3-observed-htrf-binding-trka; uc-binder-20261022-eval-alphaproteo-s3-observed-htrf-binding-vegfa; uc-binder-20261022-eval-alphaproteo-s3-subcloned-expressed-bhrf1; uc-binder-20261022-eval-alphaproteo-s3-subcloned-expressed-il17a; uc-binder-20261022-eval-alphaproteo-s3-subcloned-expressed-il7ra; uc-binder-20261022-eval-alphaproteo-s3-subcloned-expressed-pdl1; uc-binder-20261022-eval-alphaproteo-s3-subcloned-expressed-sc2rbd; uc-binder-20261022-eval-alphaproteo-s3-subcloned-expressed-trka; uc-binder-20261022-eval-alphaproteo-s3-subcloned-expressed-vegfa; uc-binder-20261022-eval-alphaproteo-s3-tested-htrf-bhrf1; uc-binder-20261022-eval-alphaproteo-s3-tested-htrf-il17a; uc-binder-20261022-eval-alphaproteo-s3-tested-htrf-il7ra; uc-binder-20261022-eval-alphaproteo-s3-tested-htrf-pdl1; uc-binder-20261022-eval-alphaproteo-s3-tested-htrf-sc2rbd; uc-binder-20261022-eval-alphaproteo-s3-tested-htrf-trka; uc-binder-20261022-eval-alphaproteo-s3-tested-htrf-vegfa; uc-binder-20261022-eval-alphaproteo-s3-yeast-hits-selected-bhrf1; uc-binder-20261022-eval-alphaproteo-s3-yeast-hits-selected-il17a; uc-binder-20261022-eval-alphaproteo-s3-yeast-hits-selected-il7ra; uc-binder-20261022-eval-alphaproteo-s3-yeast-hits-selected-pdl1; uc-binder-20261022-eval-alphaproteo-s3-yeast-hits-selected-sc2rbd; uc-binder-20261022-eval-alphaproteo-s3-yeast-hits-selected-trka; uc-binder-20261022-eval-alphaproteo-s3-yeast-hits-selected-vegfa
- revision
- 1
- source locator
- uc-binder-20261022-source-alphaproteo: Table S3
- stratum label
- AlphaProteo yeast hits through E. coli expression and HTRF
- stratum order
- 1
- value
- uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel
- pins
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