Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter; Nature 2025 version of record; Supplementary Methods Table 6

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.

18 recorded evaluations, 18 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

18 evaluations · 18 results. Different protocols are not a single leaderboard.

Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter

Sorted by Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 0.0) (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	Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 0.0)	Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 0.1)	Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 1)	Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 0.0; value printed in parentheses because it repeats the 96-design row from the same design campaign)	Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 0.1; value printed in parentheses because it repeats the 96-design row from the same design campaign)	Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 1; value printed in parentheses because it repeats the 96-design row from the same design campaign)
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target TcdB	27.5% (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target IL-7 Receptor α	12.5%	Not reported	Not reported	Not reported	Not reported	Not reported
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target SARS-CoV-2 RBD	11%	Not reported	Not reported	Not reported	Not reported	Not reported
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target Influenza Hemagglutinin	3.5%	Not reported	Not reported	Not reported	Not reported	Not reported
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target RSV-F Site III	1%	Not reported	Not reported	Not reported	Not reported	Not reported
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target Influenza Hemagglutinin	Not reported	7.5%	Not reported	Not reported	Not reported	Not reported
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target Influenza Hemagglutinin	Not reported	Not reported	11.5%	Not reported	Not reported	Not reported
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target Influenza Hemagglutinin	Not reported	Not reported	Not reported	(3.5)%	Not reported	Not reported
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target Influenza Hemagglutinin	Not reported	Not reported	Not reported	Not reported	(7.5)%	Not reported
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target Influenza Hemagglutinin	Not reported	Not reported	Not reported	Not reported	Not reported	(11.5)%
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target IL-7 Receptor α	Not reported	27%	Not reported	Not reported	Not reported	Not reported
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target IL-7 Receptor α	Not reported	Not reported	34.5%	Not reported	Not reported	Not reported
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target SARS-CoV-2 RBD	Not reported	23.5%	Not reported	Not reported	Not reported	Not reported
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target SARS-CoV-2 RBD	Not reported	Not reported	28%	Not reported	Not reported	Not reported
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target RSV-F Site III	Not reported	3%	Not reported	Not reported	Not reported	Not reported
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target RSV-F Site III	Not reported	Not reported	25%	Not reported	Not reported	Not reported
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target TcdB	Not reported	33.5% (best in column)	Not reported	Not reported	Not reported	Not reported
Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1Evaluation	Bennett VHH design target TcdB	Not reported	Not reported	41% (best in column)	Not reported	Not reported	Not reported

All 18 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: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target Influenza Hemagglutinin	3.5% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 0.0) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against H1 stem, fine-tuned RoseTTAFold2 filter, hotspot proportion 0.0 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'H1 stem' (Designs screened = 96), column 'Success rate (%) (RF2, hotspot proportion = 0.0)'
Configuration: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target Influenza Hemagglutinin	7.5% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 0.1) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against H1 stem, fine-tuned RoseTTAFold2 filter, hotspot proportion 0.1 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'H1 stem' (Designs screened = 96), column 'Success rate (%) (RF2, hotspot proportion = 0.1)'
Configuration: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target Influenza Hemagglutinin	11.5% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 1) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against H1 stem, fine-tuned RoseTTAFold2 filter, hotspot proportion 1 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'H1 stem' (Designs screened = 96), column 'Success rate (%) (RF2, hotspot proportion = 1)'
Configuration: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target Influenza Hemagglutinin	(3.5)% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 0.0; value printed in parentheses because it repeats the 96-design row from the same design campaign) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against H1 stem, fine-tuned RoseTTAFold2 filter, hotspot proportion 0.0 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'H1 stem' (Designs screened = 9000), column 'Success rate (%) (RF2, hotspot proportion = 0.0)'
Configuration: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target Influenza Hemagglutinin	(7.5)% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 0.1; value printed in parentheses because it repeats the 96-design row from the same design campaign) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against H1 stem, fine-tuned RoseTTAFold2 filter, hotspot proportion 0.1 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'H1 stem' (Designs screened = 9000), column 'Success rate (%) (RF2, hotspot proportion = 0.1)'
Configuration: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target Influenza Hemagglutinin	(11.5)% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 1; value printed in parentheses because it repeats the 96-design row from the same design campaign) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against H1 stem, fine-tuned RoseTTAFold2 filter, hotspot proportion 1 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'H1 stem' (Designs screened = 9000), column 'Success rate (%) (RF2, hotspot proportion = 1)'
Configuration: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target IL-7 Receptor α	12.5% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 0.0) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against IL7R, fine-tuned RoseTTAFold2 filter, hotspot proportion 0.0 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'IL7R' (Designs screened = 96), column 'Success rate (%) (RF2, hotspot proportion = 0.0)'
Configuration: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target IL-7 Receptor α	27% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 0.1) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against IL7R, fine-tuned RoseTTAFold2 filter, hotspot proportion 0.1 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'IL7R' (Designs screened = 96), column 'Success rate (%) (RF2, hotspot proportion = 0.1)'
Configuration: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target IL-7 Receptor α	34.5% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 1) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against IL7R, fine-tuned RoseTTAFold2 filter, hotspot proportion 1 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'IL7R' (Designs screened = 96), column 'Success rate (%) (RF2, hotspot proportion = 1)'
Configuration: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target SARS-CoV-2 RBD	11% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 0.0) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against SARS-CoV-2 RBD, fine-tuned RoseTTAFold2 filter, hotspot proportion 0.0 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'SARS-CoV-2 RBD' (Designs screened = 9000), column 'Success rate (%) (RF2, hotspot proportion = 0.0)'
Configuration: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target SARS-CoV-2 RBD	23.5% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 0.1) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against SARS-CoV-2 RBD, fine-tuned RoseTTAFold2 filter, hotspot proportion 0.1 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'SARS-CoV-2 RBD' (Designs screened = 9000), column 'Success rate (%) (RF2, hotspot proportion = 0.1)'
Configuration: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target SARS-CoV-2 RBD	28% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 1) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against SARS-CoV-2 RBD, fine-tuned RoseTTAFold2 filter, hotspot proportion 1 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'SARS-CoV-2 RBD' (Designs screened = 9000), column 'Success rate (%) (RF2, hotspot proportion = 1)'
Configuration: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target RSV-F Site III	1% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 0.0) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against RSV site 3, fine-tuned RoseTTAFold2 filter, hotspot proportion 0.0 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'RSV site 3' (Designs screened = 9000), column 'Success rate (%) (RF2, hotspot proportion = 0.0)'
Configuration: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target RSV-F Site III	3% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 0.1) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against RSV site 3, fine-tuned RoseTTAFold2 filter, hotspot proportion 0.1 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'RSV site 3' (Designs screened = 9000), column 'Success rate (%) (RF2, hotspot proportion = 0.1)'
Configuration: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target RSV-F Site III	25% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 1) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against RSV site 3, fine-tuned RoseTTAFold2 filter, hotspot proportion 1 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'RSV site 3' (Designs screened = 9000), column 'Success rate (%) (RF2, hotspot proportion = 1)'
Configuration: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target TcdB	27.5% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 0.0) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against TcdB, fine-tuned RoseTTAFold2 filter, hotspot proportion 0.0 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'TcdB' (Designs screened = 96), column 'Success rate (%) (RF2, hotspot proportion = 0.0)'
Configuration: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target TcdB	33.5% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 0.1) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against TcdB, fine-tuned RoseTTAFold2 filter, hotspot proportion 0.1 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'TcdB' (Designs screened = 96), column 'Success rate (%) (RF2, hotspot proportion = 0.1)'
Configuration: Fine-tuned RFdiffusion VHH design with fine-tuned RoseTTAFold2 filtering at hotspot proportion 1	Protocol: Bennett VHH computational success rate under the fine-tuned RoseTTAFold2 filter Dataset: Bennett VHH design target TcdB	41% Success rate (fine-tuned RoseTTAFold2 filter, hotspot proportion 1) 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 The main text says 'at lower throughput with Escherichia coli expression and single-concentration surface plasmon resonance (SPR; 95 designs per target; TcdB, IL-7Ra and influenza haemagglutinin)', but Supplementary Methods Table 6 prints 96 designs screened for TcdB, IL7R and H1 stem. Table 6's value is recorded because it is the chosen table; the main text figure is 95.Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Results paragraph 2; Supplementary Methods Table 6, column 'Designs screened' Methods, coverage and source Fine-tuned RFdiffusion VHH computational success rate against TcdB, fine-tuned RoseTTAFold2 filter, hotspot proportion 1 uc-binder-20261022-protocol-bennett-insilico-rf2-success Aggregation: Not reported Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6; Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Supplementary Methods Table 6, row 'TcdB' (Designs screened = 96), column 'Success rate (%) (RF2, hotspot proportion = 1)'

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Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Original source · Nature, version of record; Europe PMC JATS full text for PMC12727541
Bennett 2025 Supplementary Information, including Supplementary Methods Tables 5 and 6 · Original source · Supplementary Information PDF 41586_2025_9721_MOESM1_ESM.pdf, 129 pages, InDesign 17.4, ModDate 2026-09-15

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Technical metadata and extraction receipts

Stable ID: uc-binder-20261022-protocol-bennett-insilico-rf2-success

areas: proteins-complexes; protein-structure
contexts: research
limitations: An in silico filter pass rate, not a measured outcome.; The filter is the authors' own fine-tuned RoseTTAFold2, and the caption states that hotspot proportion 1, the setting used for filtering in the work, 'is likely not the most predictive setting'.; The H1 stem 9,000-design row repeats the 96-design row's values in parentheses, because both come from the same design campaign.
metric: success-rate
metric direction: higher
metric qualifier: computational filter pass rate, fine-tuned RoseTTAFold2, Ca RMSD below 2 A and pAE interaction below 10
protocol: 200 backbones are designed per target and the best of eight ProteinMPNN sequences per backbone is predicted with fine-tuned RoseTTAFold2. Success is defined as Ca RMSD below 2 A and pAE interaction below 10. Three levels of provided privileged information, hotspot proportion 1, 0.1 and 0.0, are reported separately.
review: artifact sha256: d7876bc73c47f2cb3fcb0fa1ef917c89c9b67750a22f6402bf515f978cd1564a; method: source-hash-verification; independent-cell-check; ai-assisted-source-review; method note: Re-downloaded from Europe PMC (HTTP 200, 169,840 bytes) and the SHA-256 recomputed and matched. Own flattening of the JATS XML. The main text's '95 designs per target' was confirmed verbatim and the string '96 designs' does not occur, so the conflict with Supplementary Methods Table 6 is real.; 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://www.ebi.ac.uk/europepmc/webservices/rest/PMC12727541/fullTextXML; reviewed at: 2026-10-22T15:00:00Z; reviewer: claude; reviewer note: Claude review agent, independent of the extraction agent; no human review claimed
scope limitations: An in silico filter pass rate, not a measured outcome. The Table 6 caption gives its purpose as providing 'an estimate of the compute requirements required to generate libraries'.
source locator: Supplementary Methods Table 6, columns 'Success rate (%) (RF2, hotspot proportion = 1 / 0.1 / 0.0)'
success threshold: criterion: Ca RMSD < 2 A and pAE Interaction < 10; locator: Supplementary Methods Table 6 caption
unit: percent
version: Nature 2025 version of record; Supplementary Methods Table 6

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