Configuration

AlphaProteo v2

AlphaProteo binder design as configured for alphaproteo v2: v2 generative model, run against PD-L1, TrkA and TNF-alpha.

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Evaluations and results

5 evaluations · 5 results. Different protocols are not a single leaderboard.

Sorted by Hit rate (yeast-display binding signal above 0.2, over designs tested) (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	Protocol and dataset	Hit rate (yeast-display binding signal above 0.2, over designs tested)	Dissociation constant (best KD by HTRF among the designs tested for this design system)
AlphaProteo v2Evaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 0.2, AlphaProteo binder design target PD-L1	26.5% (best in column)	Not reported
AlphaProteo v2Evaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 0.2, AlphaProteo binder design target TrkA	8.1%	Not reported
AlphaProteo v2Evaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 0.2, AlphaProteo binder design target TNF-alpha	0%	Not reported
AlphaProteo v2Evaluation	AlphaProteo best per-target binder affinity by HTRF, AlphaProteo binder design target PD-L1	Not reported	0.18 (best in column)
AlphaProteo v2Evaluation	AlphaProteo best per-target binder affinity by HTRF, AlphaProteo binder design target TrkA	Not reported	60

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AlphaProteo v2	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target PD-L1	26.5% Hit rate (yeast-display binding signal above 0.2, 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 v2 on PD-L1 (yeast-display hit rate, Table S2) uc-binder-20261022-protocol-alphaproteo-yeast-display-signal-0-2 Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S2, 'Success (%)' block, row 'AlphaProteo v2', column 'PD-L1'
Configuration: AlphaProteo v2	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target TNF-alpha	0% Hit rate (yeast-display binding signal above 0.2, 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 v2 on TNF-alpha (yeast-display hit rate, Table S2) uc-binder-20261022-protocol-alphaproteo-yeast-display-signal-0-2 Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S2, 'Success (%)' block, row 'AlphaProteo v2', column 'TNF-alpha'
Configuration: AlphaProteo v2	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target TrkA	8.1% Hit rate (yeast-display binding signal above 0.2, 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 v2 on TrkA (yeast-display hit rate, Table S2) uc-binder-20261022-protocol-alphaproteo-yeast-display-signal-0-2 Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S2, 'Success (%)' block, row 'AlphaProteo v2', column 'TrkA'
Configuration: AlphaProteo v2	Protocol: AlphaProteo best per-target binder affinity by HTRF Dataset: AlphaProteo binder design target PD-L1	0.18 Dissociation constant (best KD by HTRF among the designs tested for this design system) nanomolar · lower 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 v2 on PD-L1 (best KD by HTRF, Table S2) uc-binder-20261022-protocol-alphaproteo-htrf-kd Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S2, 'Binding KD (nM)' block, row 'AlphaProteo v2', column 'PD-L1'
Configuration: AlphaProteo v2	Protocol: AlphaProteo best per-target binder affinity by HTRF Dataset: AlphaProteo binder design target TrkA	60 Dissociation constant (best KD by HTRF among the designs tested for this design system) nanomolar · lower 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 v2 on TrkA (best KD by HTRF, Table S2) uc-binder-20261022-protocol-alphaproteo-htrf-kd Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S2, 'Binding KD (nM)' block, row 'AlphaProteo v2', column 'TrkA'

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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: uc-binder-20261022-config-alphaproteo-v2

areas: proteins-complexes; protein-structure
contexts: research
method types: specialist
access reuse: Closed system; run by the authors. Not available to reuse.
foundation model eligible: false
method role: design
parameters: v2 generative model, run against PD-L1, TrkA and TNF-alpha
reported name: AlphaProteo v2
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: Table S2, rows 'AlphaProteo v2'; Section S2
version: arXiv:2409.08022v1

Related records

configuration of: AlphaProteo
system: AlphaProteo v2 on PD-L1 (best KD by HTRF, Table S2)
system: AlphaProteo v2 on TrkA (best KD by HTRF, Table S2)
system: AlphaProteo v2 on PD-L1 (yeast-display hit rate, Table S2)
system: AlphaProteo v2 on TNF-alpha (yeast-display hit rate, Table S2)
system: AlphaProteo v2 on TrkA (yeast-display hit rate, Table S2)

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