Protocol

AlphaProteo yeast-display binding screen, hit at binding signal above 1.3 (IL-17A)

Share of tested binder designs whose yeast-display flow-cytometry binding signal exceeds 1.3, the threshold used for IL-17A.

2 evaluations · 2 results

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2 recorded evaluations, 2 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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All evaluations

2 evaluations · 2 results. Different protocols are not a single leaderboard.

Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 1.3 (IL-17A) · Dataset: AlphaProteo binder design target IL-17A

Sorted by Hit rate (yeast-display binding signal above 1.3, over designs tested; pooled over the AlphaProteo design systems tested for this target) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Hit rate (yeast-display binding signal above 1.3, over designs tested; pooled over the AlphaProteo design systems tested for this target)	Hit rate (yeast-display binding signal above 1.3, over designs tested)
AlphaProteo, pooled over tested design systemsEvaluation	14%	Not reported
AlphaProteo v1Evaluation	Not reported	14.3%

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AlphaProteo v1	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 1.3 (IL-17A) Dataset: AlphaProteo binder design target IL-17A	14.3% Hit rate (yeast-display binding signal above 1.3, over designs tested) percent · higher Uncertainty: Not reported by the source: No interval is printed. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo v1 on IL-17A (yeast-display hit rate, Table S2) uc-binder-20261022-protocol-alphaproteo-yeast-display-signal-1-3 Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S2, 'Success (%)' block, row 'AlphaProteo v1', column 'IL-17A'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 1.3 (IL-17A) Dataset: AlphaProteo binder design target IL-17A	14% Hit rate (yeast-display binding signal above 1.3, over designs tested; pooled over the AlphaProteo design systems tested for this target) percent · higher Uncertainty: Not reported by the source: No interval or replicate count is printed. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo on IL-17A, pooled over tested design systems (yeast-display hit rate, Table 1) uc-binder-20261022-protocol-alphaproteo-yeast-display-signal-1-3 Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1, 'Experimental success rate (%)' block, row 'AlphaProteo', column 'IL-17A'

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Author-reported evaluations: 2

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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: uc-binder-20261022-protocol-alphaproteo-yeast-display-signal-1-3

areas: proteins-complexes; protein-structure
contexts: research
comparison limit: A different hit threshold from the other seven targets, so IL-17A rates are not comparable with them.
limitations: Developer-reported: the authors built AlphaProteo, chose the targets, ran the assay and chose which designs to test.; A hit is a flow-cytometry binding signal above a manually calibrated threshold, not an affinity. The thresholds 'were calibrated manually by visually inspecting scatterplots of the raw yeast data' (Section S1.2.1).; The designs tested were chosen by the authors' own automated filter from a larger in silico set, so the design step and the selection step are coupled.; Denominators are small (30 to 172 designs per target) and no uncertainty is printed.; No conventional comparator (directed evolution, display selection or grafting) was run on these targets.; Target concentrations were 0.5 to 1 micromolar, 10- to 20-fold lower than in the RFdiffusion publication, 'which may exclude lower-affinity hits' (Section S4.1).
metric: hit-rate
metric direction: higher
metric qualifier: yeast-display binding signal above 1.3, over designs tested
protocol: As the 0.2-threshold screen, but with the binding-signal threshold set to 1.3 'to account for background binding' on IL-17A. For VEGF-A and IL-17A an avidity method with increased sensitivity was used, in which target proteins were pre-incubated with FITC antibody and streptavidin-phycoerythrin before incubation with cells.
review: artifact sha256: 953b35644c0fa06ff090d7614c2e19525831f8fde50242e176d54474133c5a42; method: source-hash-verification; 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
source locator: Section S1.2.1; Table 1, column 'IL-17A'
success threshold: criterion: yeast-display flow-cytometry binding signal > 1.3; locator: Section S1.2.1; scope: IL-17A only
unit: percent
version: arXiv:2409.08022v1 Section S1.2.1

Related records

assessment: AlphaProteo v1 on IL-17A (yeast-display hit rate, Table S2)
assessment: AlphaProteo on IL-17A, pooled over tested design systems (yeast-display hit rate, Table 1)
assessed by: Design a new binder to a chosen target

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