Configuration

AlphaProteo v1

AlphaProteo binder design as configured for alphaproteo v1: v1 generative model with the original automated filter; between 47 and 172 candidates chosen per target from a larger in silico set.

17 evaluations · 17 results

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.

Evaluations and results

17 evaluations · 17 results. Different protocols are not a single leaderboard.

Sorted by Dissociation constant (best KD by HTRF among the designs tested for this design system) (lower 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	Dissociation constant (best KD by HTRF among the designs tested for this design system)	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; hotspot conditioning)	Dissociation constant (best KD by HTRF among the designs tested for this design system; subset made without hotspot conditioning, marked with a dagger)	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)	Hit rate (yeast-display binding signal above 1.3, over designs tested)
AlphaProteo v1Evaluation	AlphaProteo best per-target binder affinity by HTRF, AlphaProteo binder design target IL-7RA	0.08 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo best per-target binder affinity by HTRF, AlphaProteo binder design target VEGF-A	0.48	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo best per-target binder affinity by HTRF, AlphaProteo binder design target TrkA	0.96	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo best per-target binder affinity by HTRF, AlphaProteo binder design target PD-L1	3.4	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo best per-target binder affinity by HTRF, AlphaProteo binder design target IL-17A	8.4	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo best per-target binder affinity by HTRF, AlphaProteo binder design target BHRF1	8.5	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 0.2, AlphaProteo binder design target BHRF1	Not reported	88% (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 1.3 (IL-17A), AlphaProteo binder design target IL-17A	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	14.3%
AlphaProteo v1Evaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 0.2, AlphaProteo binder design target IL-7RA	Not reported	24.5%	Not reported	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 0.2, AlphaProteo binder design target PD-L1	Not reported	9.6%	Not reported	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 0.2, AlphaProteo binder design target SC2RBD	Not reported	Not reported	Not reported	Not reported	Not reported	8.5%	Not reported
AlphaProteo v1Evaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 0.2, AlphaProteo binder design target SC2RBD	Not reported	Not reported	Not reported	Not reported	8.5%	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 0.2, AlphaProteo binder design target TNF-alpha	Not reported	0%	Not reported	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 0.2, AlphaProteo binder design target TrkA	Not reported	9.6%	Not reported	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 0.2, AlphaProteo binder design target VEGF-A	Not reported	33%	Not reported	Not reported	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo best per-target binder affinity by HTRF, AlphaProteo binder design target SC2RBD	Not reported	Not reported	Not reported	26	Not reported	Not reported	Not reported
AlphaProteo v1Evaluation	AlphaProteo best per-target binder affinity by HTRF, AlphaProteo binder design target SC2RBD	Not reported	Not reported	30	Not reported	Not reported	Not reported	Not reported

All 17 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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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 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 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 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	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 v1	Protocol: AlphaProteo best per-target binder affinity by HTRF Dataset: AlphaProteo binder design target BHRF1	8.5 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 v1 on BHRF1 (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 v1', column 'BHRF1'
Configuration: AlphaProteo v1	Protocol: AlphaProteo best per-target binder affinity by HTRF Dataset: AlphaProteo binder design target IL-17A	8.4 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 v1 on IL-17A (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 v1', column 'IL-17A'
Configuration: AlphaProteo v1	Protocol: AlphaProteo best per-target binder affinity by HTRF Dataset: AlphaProteo binder design target IL-7RA	0.08 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 v1 on IL-7RA (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 v1', column 'IL-7RA'
Configuration: AlphaProteo v1	Protocol: AlphaProteo best per-target binder affinity by HTRF Dataset: AlphaProteo binder design target PD-L1	3.4 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 v1 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 v1', column 'PD-L1'
Configuration: AlphaProteo v1	Protocol: AlphaProteo best per-target binder affinity by HTRF Dataset: AlphaProteo binder design target SC2RBD	26 Dissociation constant (best KD by HTRF among the designs tested for this design system; subset made without hotspot conditioning, marked with a dagger) 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 v1 on SC2RBD (best KD by HTRF, Table S2, no-hotspot subset) 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 v1', column 'SC2RBD' (dagger subset)
Configuration: AlphaProteo v1	Protocol: AlphaProteo best per-target binder affinity by HTRF Dataset: AlphaProteo binder design target SC2RBD	30 Dissociation constant (best KD by HTRF among the designs tested for this design system; hotspot conditioning) 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 v1 on SC2RBD (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 v1', column 'SC2RBD'
Configuration: AlphaProteo v1	Protocol: AlphaProteo best per-target binder affinity by HTRF Dataset: AlphaProteo binder design target TrkA	0.96 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 v1 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 v1', column 'TrkA'
Configuration: AlphaProteo v1	Protocol: AlphaProteo best per-target binder affinity by HTRF Dataset: AlphaProteo binder design target VEGF-A	0.48 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 v1 on VEGF-A (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 v1', column 'VEGF-A'

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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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Stable ID: uc-binder-20261022-config-alphaproteo-v1

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: v1 generative model with the original automated filter; between 47 and 172 candidates chosen per target from a larger in silico set
reported name: AlphaProteo v1
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, row 'AlphaProteo v1'; Section 2.1.1
version: arXiv:2409.08022v1

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