Protocol

Scaffold-Lab unconditional generation: Designability(↑)

Share of generated backbones that are designable. 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: Designability(↑) · Dataset: Scaffold-Lab generated backbones (100 per length group)

Sorted by Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 100) (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	Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 100)	Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 50)	Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 200)	Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 300)	Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 400)	Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 500)	Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 1000)	Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 600)	Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 800)
RFdiffusion (Scaffold-Lab unconditional generation)Evaluation	0.956 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameFlow (Scaffold-Lab unconditional generation)Evaluation	0.862	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Genie (Scaffold-Lab unconditional generation)Evaluation	0.836	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	0.799	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Chroma (Scaffold-Lab unconditional generation)Evaluation	0.763	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	0.427 (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	0.432	Not reported
Chroma (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.434
Chroma (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	0.76	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Chroma (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	0.684	Not reported	Not reported	Not reported	Not reported	Not reported
Chroma (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	0.545	Not reported	Not reported	Not reported	Not reported
Chroma (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	Not reported	0.48	Not reported	Not reported	Not reported
Chroma (Scaffold-Lab unconditional generation)Evaluation	Not reported	0.691	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	0.694	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	0.682	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	0.5	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	Not reported	0.448	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Not reported	0.781	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameFlow (Scaffold-Lab unconditional generation)Evaluation	Not reported	0.807	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Genie (Scaffold-Lab unconditional generation)Evaluation	Not reported	0.841 (best in column)	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	0.384	Not reported	Not reported
RFdiffusion (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.654 (best in column)	Not reported
RFdiffusion (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.465 (best in column)
RFdiffusion (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	0.952 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
RFdiffusion (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	0.884 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported
RFdiffusion (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	0.827 (best in column)	Not reported	Not reported	Not reported	Not reported
RFdiffusion (Scaffold-Lab unconditional generation)Evaluation	Not reported	Not reported	Not reported	Not reported	Not reported	0.722 (best in column)	Not reported	Not reported	Not reported
RFdiffusion (Scaffold-Lab unconditional generation)Evaluation	Not reported	0.726	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: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.427 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 1000) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 1000 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.432 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 600) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 600 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.434 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 800) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 800 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.76 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 200) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 200 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.684 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 300) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 300 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.545 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 400) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 400 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.48 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 500) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 500 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.763 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 100) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 100 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.691 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 50) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 50 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.694 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 200) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 200 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.682 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 300) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 300 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.5 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 400) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 400 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.448 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 500) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 500 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.799 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 100) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 100 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.781 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 50) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 50 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: FrameFlow (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.862 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 100) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 100 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: FrameFlow (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.807 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 50) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 50 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: Genie (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.836 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 100) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 100 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: Genie (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.841 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 50) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 50 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.384 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 1000) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 1000 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.654 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 600) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 600 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.465 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 800) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 800 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.952 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 200) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 200 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.884 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 300) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 300 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.827 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 400) fraction · higher 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 Designability(↑) on Scaffold-Lab unconditional generation, length 400 lit-structure-20261011-scaffoldlab-protocol-designability 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 'Designability(↑)'

Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Explore all linked results

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

External evaluations: 28

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Select a task-valid null control after reviewing inputs and metric

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Select an upstream conventional reference after reviewing the full protocol

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-23-5347695500ed. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-23-5347695500ed
Property and statement	Original source and location	Review and provenance

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

Sources and history

Release 2026-10-23-5347695500ed · Record review: source checked

1 source record and release history

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)

Download this release (gzip)

Technical metadata and extraction receipts

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

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: designability
metric direction: higher
unit: fraction
metric qualifier: Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition
version: As published 2026
source locator: Table 3, column 'Designability(↑)'; 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.

Related records

Suggest a correction