Configuration

Genie (Scaffold-Lab unconditional generation)

Configuration of Genie: Diffusion-based method, released 2023-01; run inside the Scaffold-Lab pipeline on shared hardware.

12 evaluations · 12 results

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Evaluations and results

12 evaluations · 12 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 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 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 50)	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 50)	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 50)	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 50)
Genie (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Designability(↑)	0.836	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Genie (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	0.551	Not reported
Genie (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	0.377
Genie (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Designability(↑)	Not reported	0.841	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Genie (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Diversity (↑)	Not reported	Not reported	0.83	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Genie (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Diversity (↑)	Not reported	Not reported	Not reported	0.59	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Genie (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Efficiency (↓)	Not reported	Not reported	Not reported	Not reported	Not reported	8.08	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Genie (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Efficiency (↓)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	7.92	Not reported	Not reported	Not reported	Not reported	Not reported
Genie (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	0.464	Not reported	Not reported
Genie (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Novelty(↓)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.607	Not reported	Not reported	Not reported	Not reported
Genie (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	0.715	Not reported	Not reported	Not reported
Genie (Scaffold-Lab unconditional generation)Evaluation	Scaffold-Lab unconditional generation: Rank	Not reported	Not reported	Not reported	Not reported	2	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported

All 12 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
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: Genie (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.836 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 100) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Genie Designability(↑) on Scaffold-Lab unconditional generation, length 100 lit-structure-20261011-scaffoldlab-protocol-designability Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Short' / 'Genie' / length 100, column 'Designability(↑)'
Configuration: Genie (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Designability(↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.841 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 50) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Genie Designability(↑) on Scaffold-Lab unconditional generation, length 50 lit-structure-20261011-scaffoldlab-protocol-designability Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Short' / 'Genie' / length 50, column 'Designability(↑)'
Configuration: Genie (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Diversity (↑) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.83 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 Genie 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' / 'Genie' / length 100, column 'Diversity (↑)'
Configuration: Genie (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 50) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Genie 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' / 'Genie' / length 50, column 'Diversity (↑)'
Configuration: Genie (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	8.08 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 100) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Genie Efficiency (↓) on Scaffold-Lab unconditional generation, length 100 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Short' / 'Genie' / length 100, column 'Efficiency (↓)'
Configuration: Genie (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Efficiency (↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	7.92 Runtime (average time taken to generate each backbone over 100 backbones per group, on identical hardware; length 50) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Genie Efficiency (↓) on Scaffold-Lab unconditional generation, length 50 lit-structure-20261011-scaffoldlab-protocol-efficiency Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Short' / 'Genie' / length 50, column 'Efficiency (↓)'
Configuration: Genie (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Mean Ci Dataset: Scaffold-Lab generated backbones (100 per length group)	0.464 Topsis relative closeness (TOPSIS relative closeness with CRITIC weights, mean over the lengths in the group; Short 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 Genie Mean Ci on Scaffold-Lab unconditional generation, Short 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 'Short' / 'Genie', column 'Mean Ci'
Configuration: Genie (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Novelty(↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.607 TM score (novelty as the pdb-TM of designable backbones against the PDB (lower is more novel); group mean without data preprocessing; length 100) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Genie Novelty(↓) on Scaffold-Lab unconditional generation, length 100 lit-structure-20261011-scaffoldlab-protocol-novelty 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 'Novelty(↓)'
Configuration: Genie (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Novelty(↓) Dataset: Scaffold-Lab generated backbones (100 per length group)	0.715 TM score (novelty as the pdb-TM of designable backbones against the PDB (lower is more novel); group mean without data preprocessing; length 50) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Genie Novelty(↓) on Scaffold-Lab unconditional generation, length 50 lit-structure-20261011-scaffoldlab-protocol-novelty 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 'Novelty(↓)'
Configuration: Genie (Scaffold-Lab unconditional generation)	Protocol: Scaffold-Lab unconditional generation: Rank Dataset: Scaffold-Lab generated backbones (100 per length group)	2 Rank (rank within the length group by mean TOPSIS relative closeness; Short group) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 3 Designability column: equation (1) defines a per-backbone success over 100 backbones per length, which gives two-decimal fractions, but the column prints three-decimal group means; the aggregation behind the column is not stated, and the criterion is sc-TM above 0.5, not the 2 Angstrom sc-RMSD in the store's designability concept. Do not compare these values with other designability results.Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, column 'Designability(↑)'; Metrics, equation (1) Methods, coverage and source Genie Rank on Scaffold-Lab unconditional generation, Short group lit-structure-20261011-scaffoldlab-protocol-rank Aggregation: Not reported Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Short' / 'Genie', column 'Rank'

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

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Stable ID: lit-structure-20261011-scaffoldlab-config-genie

areas: protein-structure
contexts: research
method types: specialist
reported name: Genie
reported configuration: Diffusion-based method, released 2023-01; run inside the Scaffold-Lab pipeline on shared hardware
source locator: Table 1, row 'Genie'; Table 3 row labels
missing metadata: version: reason: unreported; note: Table 1 gives the repository and release date, not a version
provenance note: Genie as run in the Scaffold-Lab unconditional generation benchmark, with ProteinMPNN sequence design and ESMFold refolding.

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