Protocol

Scaffold-Lab unconditional generation: Efficiency (↓)

Average generation time per backbone. Measured in the Scaffold-Lab unconditional generation pipeline: 100 backbones per length, 10 ProteinMPNN sequences each, refolded with ESMFold.

28 evaluations · 28 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.

28 recorded evaluations, 28 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

28 evaluations · 28 results. Different protocols are not a single leaderboard.

Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) · Dataset: Scaffold-Lab generated backbones (100 per length group)

Sorted by Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 100) (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	Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 100)	Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 50)	Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 200)	Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 300)	Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 400)	Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 500)	Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 1000)	Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 600)	Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 800)
FrameFlow (Scaffold-Lab unconditional generation)Evaluation	0.17 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
RFdiffusion (Scaffold-Lab unconditional generation)Evaluation	1.05	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	1.71	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Chroma (Scaffold-Lab unconditional generation)Evaluation	2.73	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Genie (Scaffold-Lab unconditional generation)Evaluation	8.08	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Chroma (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	24.7 (best in column)	Not reported	Not reported
Chroma (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	12.2 (best in column)	Not reported
Chroma (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	19.3 (best in column)
Chroma (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	4.68	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Chroma (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	5.73	Not reported	Not reported	Not reported	Not reported	Not reported
Chroma (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	6.92	Not reported	Not reported	Not reported	Not reported
Chroma (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	Not reported	8.56	Not reported	Not reported	Not reported
Chroma (Scaffold-Lab unconditional generation)Evaluation	Not reported	1.17	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	1.82 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	2.38 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	3.27 (best in column)	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	Not reported	4.7 (best in column)	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Not reported	0.44	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameFlow (Scaffold-Lab unconditional generation)Evaluation	Not reported	0.11 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Genie (Scaffold-Lab unconditional generation)Evaluation	Not reported	7.92	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
RFdiffusion (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	54.4	Not reported	Not reported
RFdiffusion (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	20.3	Not reported
RFdiffusion (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	37.4
RFdiffusion (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	2.54	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
RFdiffusion (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	6.32	Not reported	Not reported	Not reported	Not reported	Not reported
RFdiffusion (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	10.3	Not reported	Not reported	Not reported	Not reported
RFdiffusion (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	Not reported	14	Not reported	Not reported	Not reported
RFdiffusion (Scaffold-Lab unconditional generation)Evaluation	Not reported	0.54	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported

All 28 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: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	24.7 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 1000) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Chroma Efficiency (↓) on Scaffold-Lab unconditional generation, length 1000 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Long' / 'Chroma' / length 1000, column 'Efficiency (↓)'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	12.2 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 600) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Chroma Efficiency (↓) on Scaffold-Lab unconditional generation, length 600 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Long' / 'Chroma' / length 600, column 'Efficiency (↓)'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	19.3 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 800) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Chroma Efficiency (↓) on Scaffold-Lab unconditional generation, length 800 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Long' / 'Chroma' / length 800, column 'Efficiency (↓)'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	4.68 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 200) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Chroma Efficiency (↓) on Scaffold-Lab unconditional generation, length 200 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Medium' / 'Chroma' / length 200, column 'Efficiency (↓)'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	5.73 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 300) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Chroma Efficiency (↓) on Scaffold-Lab unconditional generation, length 300 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Medium' / 'Chroma' / length 300, column 'Efficiency (↓)'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	6.92 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 400) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Chroma Efficiency (↓) on Scaffold-Lab unconditional generation, length 400 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Medium' / 'Chroma' / length 400, column 'Efficiency (↓)'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	8.56 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 500) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Chroma Efficiency (↓) on Scaffold-Lab unconditional generation, length 500 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Medium' / 'Chroma' / length 500, column 'Efficiency (↓)'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	2.73 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 100) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Chroma Efficiency (↓) on Scaffold-Lab unconditional generation, length 100 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Short' / 'Chroma' / length 100, column 'Efficiency (↓)'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	1.17 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 50) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Chroma Efficiency (↓) on Scaffold-Lab unconditional generation, length 50 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Short' / 'Chroma' / length 50, column 'Efficiency (↓)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	1.82 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 200) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source FrameDiff Efficiency (↓) on Scaffold-Lab unconditional generation, length 200 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Medium' / 'FrameDiff' / length 200, column 'Efficiency (↓)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	2.38 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 300) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source FrameDiff Efficiency (↓) on Scaffold-Lab unconditional generation, length 300 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Medium' / 'FrameDiff' / length 300, column 'Efficiency (↓)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	3.27 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 400) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source FrameDiff Efficiency (↓) on Scaffold-Lab unconditional generation, length 400 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Medium' / 'FrameDiff' / length 400, column 'Efficiency (↓)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	4.7 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 500) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source FrameDiff Efficiency (↓) on Scaffold-Lab unconditional generation, length 500 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Medium' / 'FrameDiff' / length 500, column 'Efficiency (↓)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	1.71 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 100) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source FrameDiff Efficiency (↓) on Scaffold-Lab unconditional generation, length 100 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Short' / 'FrameDiff' / length 100, column 'Efficiency (↓)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.44 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 50) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source FrameDiff Efficiency (↓) on Scaffold-Lab unconditional generation, length 50 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Short' / 'FrameDiff' / length 50, column 'Efficiency (↓)'
Configuration: FrameFlow (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.17 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 100) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source FrameFlow Efficiency (↓) on Scaffold-Lab unconditional generation, length 100 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Short' / 'FrameFlow' / length 100, column 'Efficiency (↓)'
Configuration: FrameFlow (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.11 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 50) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source FrameFlow Efficiency (↓) on Scaffold-Lab unconditional generation, length 50 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Short' / 'FrameFlow' / length 50, column 'Efficiency (↓)'
Configuration: Genie (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	8.08 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 100) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Genie Efficiency (↓) on Scaffold-Lab unconditional generation, length 100 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Short' / 'Genie' / length 100, column 'Efficiency (↓)'
Configuration: Genie (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	7.92 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 50) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Genie Efficiency (↓) on Scaffold-Lab unconditional generation, length 50 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Short' / 'Genie' / length 50, column 'Efficiency (↓)'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	54.4 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 1000) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source RFdiffusion Efficiency (↓) on Scaffold-Lab unconditional generation, length 1000 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Long' / 'RFdiffusion' / length 1000, column 'Efficiency (↓)'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	20.3 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 600) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source RFdiffusion Efficiency (↓) on Scaffold-Lab unconditional generation, length 600 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Long' / 'RFdiffusion' / length 600, column 'Efficiency (↓)'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	37.4 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 800) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source RFdiffusion Efficiency (↓) on Scaffold-Lab unconditional generation, length 800 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Long' / 'RFdiffusion' / length 800, column 'Efficiency (↓)'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	2.54 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 200) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source RFdiffusion Efficiency (↓) on Scaffold-Lab unconditional generation, length 200 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Medium' / 'RFdiffusion' / length 200, column 'Efficiency (↓)'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	6.32 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 300) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source RFdiffusion Efficiency (↓) on Scaffold-Lab unconditional generation, length 300 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Medium' / 'RFdiffusion' / length 300, column 'Efficiency (↓)'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	10.3 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 400) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source RFdiffusion Efficiency (↓) on Scaffold-Lab unconditional generation, length 400 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Medium' / 'RFdiffusion' / length 400, column 'Efficiency (↓)'

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Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Original source · Version of record, PLoS Computational Biology 2026 (PMC13225634 JATS full text)

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Stable ID: lit-structure-20261011-scaffoldlab-protocol-efficiency

areas: protein-structure
contexts: research
protocol: Per method and length, 100 backbones are generated, 10 sequences are designed for each with ProteinMPNN and refolded with ESMFold; the metrics are group means without data preprocessing. Ranking uses TOPSIS with CRITIC weighting.
metric: runtime
metric direction: lower
unit: unit-unreported
metric qualifier: average time taken to generate each backbone over 100 backbones per group, on identical hardware
version: As published 2026
source locator: Table 3, column 'Efficiency (↓)'; Metrics section
aggregation: Mean within each length group without data preprocessing
limitations: Group means only; the per-backbone values are not published in the article.; Table 3 prints no unit for this column.
unit detail: average time to generate one backbone; Table 3 prints no unit

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