Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authors; Design sequences as published by Watson et al. (reference [S28]), downloaded from figshare (https://figshare.com/s/439fdd59488215753bc3)

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Evaluations and results

12 evaluations · 12 results. Different protocols are not a single leaderboard.

Sorted by Dissociation constant (best KD among the 95 published RFdiffusion designs, measured by the AlphaProteo authors using HTRF (asterisk in Table 1)) (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 among the 95 published RFdiffusion designs, measured by the AlphaProteo authors using HTRF (asterisk in Table 1))	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)	Hit rate (yeast-display binding signal above 0.2, over the 95 published RFdiffusion designs tested)
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo best per-target binder affinity by HTRF, AlphaProteo binder design target PD-L1	1.6* (best in column)	Not reported	Not reported	Not reported
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo best per-target binder affinity by HTRF, AlphaProteo binder design target IL-7RA	14*	Not reported	Not reported	Not reported
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo best per-target binder affinity by HTRF, AlphaProteo binder design target TrkA	370*	Not reported	Not reported	Not reported
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 0.2, AlphaProteo binder design target IL-7RA	Not reported	Not reported	16.8% (best in column)	Not reported
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 0.2, AlphaProteo binder design target PD-L1	Not reported	Not reported	12.6%	Not reported
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 0.2, AlphaProteo binder design target TrkA	Not reported	Not reported	0%	Not reported
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo best per-target binder affinity by HTRF, AlphaProteo binder design target IL-7RA	Not reported	14.1	Not reported	Not reported
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo best per-target binder affinity by HTRF, AlphaProteo binder design target PD-L1	Not reported	1.56 (best in column)	Not reported	Not reported
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo best per-target binder affinity by HTRF, AlphaProteo binder design target TrkA	Not reported	370	Not reported	Not reported
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 0.2, AlphaProteo binder design target IL-7RA	Not reported	Not reported	Not reported	17% (best in column)
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 0.2, AlphaProteo binder design target PD-L1	Not reported	Not reported	Not reported	13%
Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authorsEvaluation	AlphaProteo yeast-display binding screen, hit at binding signal above 0.2, AlphaProteo binder design target TrkA	Not reported	Not reported	Not reported	0%

All 12 result rows with coverage, uncertainty and sources

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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: Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authors	Protocol: AlphaProteo best per-target binder affinity by HTRF Dataset: AlphaProteo binder design target IL-7RA	14.1 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	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 (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 'RFdiffusion (our measurement)', column 'IL-7RA'
Configuration: Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authors	Protocol: AlphaProteo best per-target binder affinity by HTRF Dataset: AlphaProteo binder design target PD-L1	1.56 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	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 (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 'RFdiffusion (our measurement)', column 'PD-L1'
Configuration: Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authors	Protocol: AlphaProteo best per-target binder affinity by HTRF Dataset: AlphaProteo binder design target TrkA	370 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	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 (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 'RFdiffusion (our measurement)', column 'TrkA'
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'
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 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 TrkA, 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 'TrkA'
Configuration: Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authors	Protocol: AlphaProteo best per-target binder affinity by HTRF Dataset: AlphaProteo binder design target IL-7RA	14* Dissociation constant (best KD among the 95 published RFdiffusion designs, measured by the AlphaProteo authors using HTRF (asterisk in Table 1)) nanomolar · lower 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 (best KD by HTRF, Table 1) 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 1, 'Binding KD (nM)' block, row 'RFdiffusion', column 'IL-7RA'
Configuration: Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authors	Protocol: AlphaProteo best per-target binder affinity by HTRF Dataset: AlphaProteo binder design target PD-L1	1.6* Dissociation constant (best KD among the 95 published RFdiffusion designs, measured by the AlphaProteo authors using HTRF (asterisk in Table 1)) nanomolar · lower 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 (best KD by HTRF, Table 1) 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 1, 'Binding KD (nM)' block, row 'RFdiffusion', column 'PD-L1'
Configuration: Published RFdiffusion designs, re-synthesised and tested by the AlphaProteo authors	Protocol: AlphaProteo best per-target binder affinity by HTRF Dataset: AlphaProteo binder design target TrkA	370* Dissociation constant (best KD among the 95 published RFdiffusion designs, measured by the AlphaProteo authors using HTRF (asterisk in Table 1)) nanomolar · lower 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 TrkA, measured by the AlphaProteo authors (best KD by HTRF, Table 1) 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 1, 'Binding KD (nM)' block, row 'RFdiffusion', 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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Stable ID: uc-binder-20261022-config-rfdiffusion-published-designs-alphaproteo-yeast

areas: proteins-complexes; protein-structure
contexts: research
method types: specialist
access reuse: Design sequences published by the original authors on figshare.
foundation model eligible: false
method role: comparator
model identity note: Section S4.1: 'we downloaded sequences of the published RFdiffusion designs and synthesized and tested them by yeast display (Section S1.2) alongside our own designs.' The designs were generated and selected by the RFdiffusion authors, so this configuration shares the assay with the AlphaProteo arms but not the design or selection step.
parameters: 95 published design sequences per target for IL-7RA, PD-L1 and TrkA; no design or filtering step was run by the AlphaProteo authors
reported name: RFdiffusion (our measurement)
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 'RFdiffusion (our measurement)'; Section S4.1
version: Design sequences as published by Watson et al. (reference [S28]), downloaded from figshare (https://figshare.com/s/439fdd59488215753bc3)

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