Dataset

Scaffold-Lab generated backbones (100 per length group)

The backbones each method generated for evaluation: 100 per length, with 10 designed sequences per backbone.

Evaluation results

160 evaluations · 160 results. Different protocols are not a single leaderboard.

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: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.222 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 1000) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 1000 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.516 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 600) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 600 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.325 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 800) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 800 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.275 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 200) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 200 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.398 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 300) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 300 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.262 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 400) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 400 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.249 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 500) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 500 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.437 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 100) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 100 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: Chroma (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.368 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 50) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 50 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.524 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 200) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 200 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.486 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 300) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 300 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.378 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 400) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 400 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.209 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 500) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 500 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.353 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 100) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 100 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.378 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 50) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 50 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: FrameFlow (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.525 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 100) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 100 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: FrameFlow (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.509 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 50) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 50 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: Genie (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.551 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 100) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 100 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: Genie (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.377 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 50) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 50 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.178 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 1000) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 1000 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.689 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 600) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 600 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.351 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 800) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 800 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.558 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 200) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 200 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.51 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 300) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 300 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'
Configuration: RFdiffusion (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.541 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 400) unitless · 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 Ci on Scaffold-Lab unconditional generation, length 400 lit-structure-20261011-scaffoldlab-protocol-ci 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 'Ci'

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Release 2026-10-23-5347695500ed · Evidence verified: Not verified

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Evidence table

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5 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
Population 100 generated backbones per method and length, each with 10 ProteinMPNN sequences Context-only references	Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework Original source ↗ Results, 'The overall workflow of Scaffold-Lab': 'We generated 100 backbones with 10 sequences for each backbone to be evaluated.' Version: Version of record, PLoS Computational Biology 2026 (PMC13225634 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.population` Source artifact SHA-256: `9ff68ef80dc57d6ef85920d4d2104e86d071215ac9c74367a72b2a85669840d0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Results, 'The overall workflow of Scaffold-Lab': 'We generated 100 backbones with 10 sequences for each backbone to be evaluated.' Context-only references	Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework Original source ↗ Results, 'The overall workflow of Scaffold-Lab': 'We generated 100 backbones with 10 sequences for each backbone to be evaluated.' Version: Version of record, PLoS Computational Biology 2026 (PMC13225634 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.source_locator` Source artifact SHA-256: `9ff68ef80dc57d6ef85920d4d2104e86d071215ac9c74367a72b2a85669840d0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split Generated de novo; no held-out split Context-only references	Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework Original source ↗ Results, 'The overall workflow of Scaffold-Lab': 'We generated 100 backbones with 10 sequences for each backbone to be evaluated.' Version: Version of record, PLoS Computational Biology 2026 (PMC13225634 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.split` Source artifact SHA-256: `9ff68ef80dc57d6ef85920d4d2104e86d071215ac9c74367a72b2a85669840d0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description The backbones each method generated for evaluation: 100 per length, with 10 designed sequences per backbone. Context-only references	Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework Original source ↗ Results, 'The overall workflow of Scaffold-Lab': 'We generated 100 backbones with 10 sequences for each backbone to be evaluated.' Version: Version of record, PLoS Computational Biology 2026 (PMC13225634 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `description` Source artifact SHA-256: `9ff68ef80dc57d6ef85920d4d2104e86d071215ac9c74367a72b2a85669840d0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Name Scaffold-Lab generated backbones (100 per length group) Context-only references	Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework Original source ↗ Results, 'The overall workflow of Scaffold-Lab': 'We generated 100 backbones with 10 sequences for each backbone to be evaluated.' Version: Version of record, PLoS Computational Biology 2026 (PMC13225634 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `name` Source artifact SHA-256: `9ff68ef80dc57d6ef85920d4d2104e86d071215ac9c74367a72b2a85669840d0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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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)

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Technical metadata and extraction receipts

Stable ID: lit-structure-20261011-scaffoldlab-data-generated-backbones

areas: protein-structure
contexts: research
population: 100 generated backbones per method and length, each with 10 ProteinMPNN sequences
split: Generated de novo; no held-out split
source locator: Results, 'The overall workflow of Scaffold-Lab': 'We generated 100 backbones with 10 sequences for each backbone to be evaluated.'
missing metadata: version: reason: inapplicable; note: Backbones are generated per run rather than released as a fixed dataset

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