Configuration

FrameDiff (Scaffold-Lab unconditional generation)

Configuration of FrameDiff: Diffusion-based method, released 2023-03; run inside the Scaffold-Lab pipeline on shared hardware.

34 evaluations · 34 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.

Evaluations and results

34 evaluations · 34 results. Different protocols are not a single leaderboard.

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	Protocol and dataset	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 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 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 500)	Proportion (unique Foldseek-Cluster clusters divided by the number of backbones in the group, clustering TM-score threshold 0.5; group mean without data preprocessing; length 100)	Proportion (unique Foldseek-Cluster clusters divided by the number of backbones in the group, clustering TM-score threshold 0.5; group mean without data preprocessing; length 200)	Proportion (unique Foldseek-Cluster clusters divided by the number of backbones in the group, clustering TM-score threshold 0.5; group mean without data preprocessing; length 300)	Proportion (unique Foldseek-Cluster clusters divided by the number of backbones in the group, clustering TM-score threshold 0.5; group mean without data preprocessing; length 400)	Proportion (unique Foldseek-Cluster clusters divided by the number of backbones in the group, clustering TM-score threshold 0.5; group mean without data preprocessing; length 50)	Proportion (unique Foldseek-Cluster clusters divided by the number of backbones in the group, clustering TM-score threshold 0.5; group mean without data preprocessing; length 500)	Rank (rank within the length group by mean TOPSIS relative closeness; Medium group)	Rank (rank within the length group by mean TOPSIS relative closeness; Short group)	Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 100)	Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 200)	Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 300)	Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 400)	Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 50)	Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 500)	TM score (novelty as the pdb-TM of designable backbones against the PDB (lower is more novel); group mean without data preprocessing; length 100)	TM score (novelty as the pdb-TM of designable backbones against the PDB (lower is more novel); group mean without data preprocessing; length 200)	TM score (novelty as the pdb-TM of designable backbones against the PDB (lower is more novel); group mean without data preprocessing; length 300)	TM score (novelty as the pdb-TM of designable backbones against the PDB (lower is more novel); group mean without data preprocessing; length 400)	TM score (novelty as the pdb-TM of designable backbones against the PDB (lower is more novel); group mean without data preprocessing; length 50)	TM score (novelty as the pdb-TM of designable backbones against the PDB (lower is more novel); group mean without data preprocessing; length 500)	Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, mean over the lengths in the group; Medium group)	Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, mean over the lengths in the group; Short group)	Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 100)	Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 200)	Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 300)	Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 400)	Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 50)	Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, per length; length 500)
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Designability(↑)	0.799	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Ci	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.524	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Ci	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.486	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Ci	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.378	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Ci	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.209
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Ci	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.353	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Ci	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.378	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Designability(↑)	Not reported	0.694	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Designability(↑)	Not reported	Not reported	0.682	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Designability(↑)	Not reported	Not reported	Not reported	0.5	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Designability(↑)	Not reported	Not reported	Not reported	Not reported	Not reported	0.448	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Designability(↑)	Not reported	Not reported	Not reported	Not reported	0.781	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Diversity (↑)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.39	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Diversity (↑)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.48	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Diversity (↑)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.55	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Diversity (↑)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.59	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Diversity (↑)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.46	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Diversity (↑)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.49	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Efficiency (↓)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	1.82	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Efficiency (↓)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	2.38	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Efficiency (↓)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	3.27	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Efficiency (↓)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	4.7	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Efficiency (↓)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	1.71	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Efficiency (↓)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.44	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Mean Ci	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.399	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Mean Ci	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.365	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Novelty(↓)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.666	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Novelty(↓)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.656	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Novelty(↓)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.654	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Novelty(↓)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.69	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Novelty(↓)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.711	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Novelty(↓)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.731	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Rank	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	2	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FrameDiff (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Rank	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	4	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported

All 34 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: 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: 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: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Diversity (↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.39 Proportion (unique Foldseek-Cluster clusters divided by the number of backbones in the group, clustering TM-score threshold 0.5; group mean without data preprocessing; 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 Diversity (↑) on Scaffold-Lab unconditional generation, length 200 lit-structure-20261011-scaffoldlab-protocol-diversity 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 'Diversity (↑)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Diversity (↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.48 Proportion (unique Foldseek-Cluster clusters divided by the number of backbones in the group, clustering TM-score threshold 0.5; group mean without data preprocessing; 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 Diversity (↑) on Scaffold-Lab unconditional generation, length 300 lit-structure-20261011-scaffoldlab-protocol-diversity 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 'Diversity (↑)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Diversity (↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.55 Proportion (unique Foldseek-Cluster clusters divided by the number of backbones in the group, clustering TM-score threshold 0.5; group mean without data preprocessing; 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 Diversity (↑) on Scaffold-Lab unconditional generation, length 400 lit-structure-20261011-scaffoldlab-protocol-diversity 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 'Diversity (↑)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Diversity (↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.59 Proportion (unique Foldseek-Cluster clusters divided by the number of backbones in the group, clustering TM-score threshold 0.5; group mean without data preprocessing; 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 Diversity (↑) on Scaffold-Lab unconditional generation, length 500 lit-structure-20261011-scaffoldlab-protocol-diversity 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 'Diversity (↑)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Diversity (↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.46 Proportion (unique Foldseek-Cluster clusters divided by the number of backbones in the group, clustering TM-score threshold 0.5; group mean without data preprocessing; 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 Diversity (↑) on Scaffold-Lab unconditional generation, length 100 lit-structure-20261011-scaffoldlab-protocol-diversity 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 'Diversity (↑)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Diversity (↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.49 Proportion (unique Foldseek-Cluster clusters divided by the number of backbones in the group, clustering TM-score threshold 0.5; group mean without data preprocessing; 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 Diversity (↑) on Scaffold-Lab unconditional generation, length 50 lit-structure-20261011-scaffoldlab-protocol-diversity 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 'Diversity (↑)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	1.82 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 200) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source FrameDiff Efficiency (↓) on Scaffold-Lab unconditional generation, length 200 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Medium' / 'FrameDiff' / length 200, column 'Efficiency (↓)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	2.38 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 300) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source FrameDiff Efficiency (↓) on Scaffold-Lab unconditional generation, length 300 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Medium' / 'FrameDiff' / length 300, column 'Efficiency (↓)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	3.27 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 400) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source FrameDiff Efficiency (↓) on Scaffold-Lab unconditional generation, length 400 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Medium' / 'FrameDiff' / length 400, column 'Efficiency (↓)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	4.7 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 500) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source FrameDiff Efficiency (↓) on Scaffold-Lab unconditional generation, length 500 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Medium' / 'FrameDiff' / length 500, column 'Efficiency (↓)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	1.71 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 100) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source FrameDiff Efficiency (↓) on Scaffold-Lab unconditional generation, length 100 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Short' / 'FrameDiff' / length 100, column 'Efficiency (↓)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.44 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 50) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source FrameDiff Efficiency (↓) on Scaffold-Lab unconditional generation, length 50 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Short' / 'FrameDiff' / length 50, column 'Efficiency (↓)'
Configuration: FrameDiff (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Mean Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.399 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, mean over the lengths in the group; Medium group) 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 Mean Ci on Scaffold-Lab unconditional generation, Medium group lit-structure-20261011-scaffoldlab-protocol-mean-ci Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Medium' / 'FrameDiff', column 'Mean Ci'

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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-config-framediff

areas: protein-structure
contexts: research
method types: specialist
reported name: FrameDiff
reported configuration: Diffusion-based method, released 2023-03; run inside the Scaffold-Lab pipeline on shared hardware
source locator: Table 1, row 'FrameDiff'; Table 3 row labels
missing metadata: version: reason: unreported; note: Table 1 gives the repository and release date, not a version
provenance note: FrameDiff as run in the Scaffold-Lab unconditional generation benchmark, with ProteinMPNN sequence design and ESMFold refolding.

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