Protocol

AlphaProteo yeast-display binding screen, hit at binding signal above 0.2

Share of tested binder designs whose yeast-display flow-cytometry binding signal exceeds 0.2.

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

26 recorded evaluations, 26 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

26 evaluations · 26 results. Different protocols are not a single leaderboard.

Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2

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)	Hit rate (yeast-display binding signal above 0.2, over designs tested; pooled over the AlphaProteo design systems tested for this target)	Hit rate (yeast-display binding signal above 0.2, over the 95 published RFdiffusion designs tested)	Hit rate (yeast-display binding signal above 0.2, over designs tested; hotspot conditioning)	Hit rate (yeast-display binding signal above 0.2, over designs tested; subset made without hotspot conditioning, marked with a dagger)
AlphaProteo v1Evaluation	AlphaProteo binder design target BHRF1	88% (best in column)	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo binder design target VEGF-A	33%	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1 with improved filtersEvaluation	AlphaProteo binder design target SC2RBD	29%	Not reported	Not reported	Not reported	Not reported
AlphaProteo v2Evaluation	AlphaProteo binder design target PD-L1	26.5%	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo binder design target IL-7RA	24.5%	Not reported	Not reported	Not reported	Not reported
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo binder design target IL-7RA	16.8%	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1 with improved filtersEvaluation	AlphaProteo binder design target PD-L1	16.1%	Not reported	Not reported	Not reported	Not reported
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo binder design target PD-L1	12.6%	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo binder design target PD-L1	9.6%	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo binder design target TrkA	9.6%	Not reported	Not reported	Not reported	Not reported
AlphaProteo v2Evaluation	AlphaProteo binder design target TrkA	8.1%	Not reported	Not reported	Not reported	Not reported
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo binder design target TrkA	0%	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo binder design target TNF-alpha	0%	Not reported	Not reported	Not reported	Not reported
AlphaProteo v2Evaluation	AlphaProteo binder design target TNF-alpha	0%	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo binder design target SC2RBD	Not reported	Not reported	Not reported	Not reported	8.5%
AlphaProteo v1Evaluation	AlphaProteo binder design target SC2RBD	Not reported	Not reported	Not reported	8.5%	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target BHRF1	Not reported	88% (best in column)	Not reported	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target IL-7RA	Not reported	25%	Not reported	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target PD-L1	Not reported	15%	Not reported	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target SC2RBD	Not reported	12%	Not reported	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target TNF-alpha	Not reported	0%	Not reported	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target TrkA	Not reported	9%	Not reported	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target VEGF-A	Not reported	33%	Not reported	Not reported	Not reported
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo binder design target IL-7RA	Not reported	Not reported	17% (best in column)	Not reported	Not reported
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo binder design target PD-L1	Not reported	Not reported	13%	Not reported	Not reported
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo binder design target TrkA	Not reported	Not reported	0%	Not reported	Not reported

All 26 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authors	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target IL-7RA	16.8% 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	Independent external 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 Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authors on IL-7RA (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 'RFdiffusion (our measurement)', column 'IL-7RA'
Configuration: Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authors	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target PD-L1	12.6% 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	Independent external 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 Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authors 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 'RFdiffusion (our measurement)', column 'PD-L1'
Configuration: Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authors	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target TrkA	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	Independent external 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 Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authors 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 'RFdiffusion (our measurement)', column 'TrkA'
Configuration: AlphaProteo v1	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target BHRF1	88% 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 v1 on BHRF1 (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 v1', column 'BHRF1'
Configuration: AlphaProteo v1	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target IL-7RA	24.5% 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 v1 on IL-7RA (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 v1', column 'IL-7RA'
Configuration: AlphaProteo v1 with improved filters	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target PD-L1	16.1% 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 v1 with improved filters 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 v1 with improved filters', column 'PD-L1'
Configuration: AlphaProteo v1 with improved filters	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target SC2RBD	29% 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 v1 with improved filters on SC2RBD (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 v1 with improved filters', column 'SC2RBD'
Configuration: AlphaProteo v1	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target PD-L1	9.6% 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 v1 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 v1', column 'PD-L1'
Configuration: AlphaProteo v1	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target SC2RBD	8.5% Hit rate (yeast-display binding signal above 0.2, over designs tested; subset made without hotspot conditioning, marked with a dagger) 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 SC2RBD (yeast-display hit rate, Table S2, no-hotspot subset) 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 v1', column 'SC2RBD' (dagger subset)
Configuration: AlphaProteo v1	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target SC2RBD	8.5% Hit rate (yeast-display binding signal above 0.2, over designs tested; hotspot conditioning) 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 SC2RBD (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 v1', column 'SC2RBD'
Configuration: AlphaProteo v1	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 v1 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 v1', column 'TNF-alpha'
Configuration: AlphaProteo v1	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target TrkA	9.6% 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 v1 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 v1', column 'TrkA'
Configuration: AlphaProteo v1	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target VEGF-A	33% 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 v1 on VEGF-A (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 v1', column 'VEGF-A'
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, pooled over tested design systems	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target BHRF1	88% Hit rate (yeast-display binding signal above 0.2, 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 BHRF1, pooled over tested design systems (yeast-display hit rate, Table 1) 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 1, 'Experimental success rate (%)' block, row 'AlphaProteo', column 'BHRF1'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target IL-7RA	25% Hit rate (yeast-display binding signal above 0.2, 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-7RA, pooled over tested design systems (yeast-display hit rate, Table 1) 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 1, 'Experimental success rate (%)' block, row 'AlphaProteo', column 'IL-7RA'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target PD-L1	15% Hit rate (yeast-display binding signal above 0.2, 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 PD-L1, pooled over tested design systems (yeast-display hit rate, Table 1) 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 1, 'Experimental success rate (%)' block, row 'AlphaProteo', column 'PD-L1'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target SC2RBD	12% Hit rate (yeast-display binding signal above 0.2, 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 SC2RBD, pooled over tested design systems (yeast-display hit rate, Table 1) 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 1, 'Experimental success rate (%)' block, row 'AlphaProteo', column 'SC2RBD'
Configuration: AlphaProteo, pooled over tested design systems	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; 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 TNF-alpha, pooled over tested design systems (yeast-display hit rate, Table 1) 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 1, 'Experimental success rate (%)' block, row 'AlphaProteo', column 'TNF-alpha'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target TrkA	9% Hit rate (yeast-display binding signal above 0.2, 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 TrkA, pooled over tested design systems (yeast-display hit rate, Table 1) 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 1, 'Experimental success rate (%)' block, row 'AlphaProteo', column 'TrkA'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target VEGF-A	33% Hit rate (yeast-display binding signal above 0.2, 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 VEGF-A, pooled over tested design systems (yeast-display hit rate, Table 1) 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 1, 'Experimental success rate (%)' block, row 'AlphaProteo', column 'VEGF-A'
Configuration: Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authors	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target IL-7RA	17% Hit rate (yeast-display binding signal above 0.2, over the 95 published RFdiffusion designs tested) percent · higher Uncertainty: Not reported by the source: No interval is printed. Coverage: Not reported scored / Not reported eligible	Independent external 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 Published RFdiffusion designs on IL-7RA, measured by the AlphaProteo authors (yeast-display hit rate, Table 1) 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 1, 'Experimental success rate (%)' block, row 'RFdiffusion', column 'IL-7RA'
Configuration: Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authors	Protocol: AlphaProteo yeast-display binding screen, hit at binding signal above 0.2 Dataset: AlphaProteo binder design target PD-L1	13% Hit rate (yeast-display binding signal above 0.2, over the 95 published RFdiffusion designs tested) percent · higher Uncertainty: Not reported by the source: No interval is printed. Coverage: Not reported scored / Not reported eligible	Independent external 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 Published RFdiffusion designs on PD-L1, measured by the AlphaProteo authors (yeast-display hit rate, Table 1) 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 1, 'Experimental success rate (%)' block, row 'RFdiffusion', column 'PD-L1'

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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-protocol-alphaproteo-yeast-display-signal-0-2

areas: proteins-complexes; protein-structure
contexts: research
control: Per-design control well with the same binder and no target, used to subtract expression-only and target-only signal shifts.
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).; Same-assay disagreement with the RFdiffusion publication. The AlphaProteo authors re-synthesised and re-tested the published RFdiffusion designs in this assay and state in Section S4.1: 'Our results matched the published success rates for PD-L1 but were 2-fold lower for IL-7RA (16% versus 33%) and 0% for TrkA (versus 6%) (Table S2).' Table S2 prints the re-tested rates as 16.8%, 12.6% and 0.0% over 95 designs against published rates of 33.7%, 12.6% and 6.3%. So this protocol reproduces the published PD-L1 rate and contradicts the published IL-7RA and TrkA rates. The published values are not recorded as results here because Watson et al. was not retrieved in this pass; they are transcribed in uc-binder-20261022-claim-alphaproteo-other-design-methods-compilation and the unretrieved primary source is a recorded gap. The authors attribute the difference to the yeast surface environment and to target concentrations 10- to 20-fold lower than in the publication.
metric: hit-rate
metric direction: higher
metric qualifier: yeast-display binding signal above 0.2, over designs tested
protocol: Designs are codon-optimised, synthesised and transformed into S. cerevisiae EBY100, displayed on the surface, incubated with biotinylated target protein, and read by flow cytometry. The binding signal is (log10 PE[FITC+,+target] - log10 PE[FITC-,+target]) - (log10 PE[FITC+,-target] - log10 PE[FITC-,-target]). Designs with a binding signal above 0.2 were considered successful binders.
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
selection: Between 47 and 172 candidates per target chosen by the authors' automated filtering procedure from a larger in silico set.
selection bias: The filter that chose the tested designs is the authors' own, so design and selection are not independent.
source locator: Section S1.2.1; Table 1; Table S2
success threshold: calibration: thresholds calibrated manually by visual inspection of raw yeast scatterplots; criterion: yeast-display flow-cytometry binding signal > 0.2; locator: Section S1.2.1
unit: percent
version: arXiv:2409.08022v1 Section S1.2.1

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