Configuration

Native PDBs

Protein model evaluated by the ProteinBench authors under their harness.

Overview

Protein model evaluated by the ProteinBench authors under their harness.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

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

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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: Native PDBs	Task: ProteinBench BB-LENGTH-100-DIVERSITY-MAX-CLUST: length 100, Diversity Max Clust. Dataset subset: Designed backbones at fixed lengths (ProteinBench split)	0.77 max-clust score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench BB-LENGTH-100-DIVERSITY-MAX-CLUST: length 100, Diversity Max Clust. Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(Native PDBs), column(length 100, Diversity Max Clust.↑)
Configuration: Native PDBs	Task: ProteinBench BB-LENGTH-100-DIVERSITY-PAIRWISE-TM: length 100, Diversity pairwise TM Dataset subset: Designed backbones at fixed lengths (ProteinBench split)	0.30 ± 0.02 pairwise-tm score · lower Uncertainty: type: standard_deviation; value: 0.02 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench BB-LENGTH-100-DIVERSITY-PAIRWISE-TM: length 100, Diversity pairwise TM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(Native PDBs), column(length 100, Diversity pairwise TM ↓)
Configuration: Native PDBs	Task: ProteinBench BB-LENGTH-100-QUALITY-SCRMSD: length 100, Quality scRMSD Dataset subset: Designed backbones at fixed lengths (ProteinBench split)	0.67 ± 1.61 scrmsd score · lower Uncertainty: type: standard_deviation; value: 1.61 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench BB-LENGTH-100-QUALITY-SCRMSD: length 100, Quality scRMSD Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(Native PDBs), column(length 100, Quality scRMSD ↓)
Configuration: Native PDBs	Task: ProteinBench BB-LENGTH-100-QUALITY-SCTM: length 100, Quality scTM Dataset subset: Designed backbones at fixed lengths (ProteinBench split)	0.96 ± 0.10 sctm score · higher Uncertainty: type: standard_deviation; value: 0.10 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench BB-LENGTH-100-QUALITY-SCTM: length 100, Quality scTM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(Native PDBs), column(length 100, Quality scTM ↑)
Configuration: Native PDBs	Task: ProteinBench BB-LENGTH-300-DIVERSITY-MAX-CLUST: length 300, Diversity Max Clust. Dataset subset: Designed backbones at fixed lengths (ProteinBench split)	0.77 max-clust score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench BB-LENGTH-300-DIVERSITY-MAX-CLUST: length 300, Diversity Max Clust. Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(Native PDBs), column(length 300, Diversity Max Clust. ↑)
Configuration: Native PDBs	Task: ProteinBench BB-LENGTH-300-DIVERSITY-PAIRWISE-TM: length 300, Diversity pairwise TM Dataset subset: Designed backbones at fixed lengths (ProteinBench split)	0.28 ± 0.02 pairwise-tm score · lower Uncertainty: type: standard_deviation; value: 0.02 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench BB-LENGTH-300-DIVERSITY-PAIRWISE-TM: length 300, Diversity pairwise TM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(Native PDBs), column(length 300, Diversity pairwise TM ↓)
Configuration: Native PDBs	Task: ProteinBench BB-LENGTH-300-QUALITY-SCRMSD: length 300, Quality scRMSD Dataset subset: Designed backbones at fixed lengths (ProteinBench split)	0.82 ± 2.67 scrmsd score · lower Uncertainty: type: standard_deviation; value: 2.67 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench BB-LENGTH-300-QUALITY-SCRMSD: length 300, Quality scRMSD Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(Native PDBs), column(length 300, Quality scRMSD ↓)
Configuration: Native PDBs	Task: ProteinBench BB-LENGTH-300-QUALITY-SCTM: length 300, Quality scTM Dataset subset: Designed backbones at fixed lengths (ProteinBench split)	0.97 ± 0.10 sctm score · higher Uncertainty: type: standard_deviation; value: 0.10 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench BB-LENGTH-300-QUALITY-SCTM: length 300, Quality scTM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(Native PDBs), column(length 300, Quality scTM ↑)
Configuration: Native PDBs	Task: ProteinBench BB-LENGTH-50-DIVERSITY-MAX-CLUST: length 50, Diversity Max Clust. Dataset subset: Designed backbones at fixed lengths (ProteinBench split)	0.66 max-clust score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench BB-LENGTH-50-DIVERSITY-MAX-CLUST: length 50, Diversity Max Clust. Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(Native PDBs), column(length 50, Diversity Max Clust. ↑)
Configuration: Native PDBs	Task: ProteinBench BB-LENGTH-50-DIVERSITY-PAIRWISE-TM: length 50, Diversity pairwise TM Dataset subset: Designed backbones at fixed lengths (ProteinBench split)	0.29 ± 0.03 pairwise-tm score · lower Uncertainty: type: standard_deviation; value: 0.03 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench BB-LENGTH-50-DIVERSITY-PAIRWISE-TM: length 50, Diversity pairwise TM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(Native PDBs), column(length 50, Diversity pairwise TM ↓)
Configuration: Native PDBs	Task: ProteinBench BB-LENGTH-50-QUALITY-SCRMSD: length 50, Quality scRMSD Dataset subset: Designed backbones at fixed lengths (ProteinBench split)	0.74 ± 1.45 scrmsd score · lower Uncertainty: type: standard_deviation; value: 1.45 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench BB-LENGTH-50-QUALITY-SCRMSD: length 50, Quality scRMSD Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(Native PDBs), column(length 50, Quality scRMSD ↓)
Configuration: Native PDBs	Task: ProteinBench BB-LENGTH-50-QUALITY-SCTM: length 50, Quality scTM Dataset subset: Designed backbones at fixed lengths (ProteinBench split)	0.91 ± 0.11 sctm score · higher Uncertainty: type: standard_deviation; value: 0.11 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench BB-LENGTH-50-QUALITY-SCTM: length 50, Quality scTM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(Native PDBs), column(length 50, Quality scTM ↑)
Configuration: Native PDBs	Task: ProteinBench BB-LENGTH-500-DIVERSITY-MAX-CLUST: length 500, Diversity Max Clust. Dataset subset: Designed backbones at fixed lengths (ProteinBench split)	0.8 max-clust score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench BB-LENGTH-500-DIVERSITY-MAX-CLUST: length 500, Diversity Max Clust. Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(Native PDBs), column(length 500, Diversity Max Clust.↑)
Configuration: Native PDBs	Task: ProteinBench BB-LENGTH-500-DIVERSITY-PAIRWISE-TM: length 500, Diversity pairwise TM Dataset subset: Designed backbones at fixed lengths (ProteinBench split)	0.29 ± 0.03 pairwise-tm score · lower Uncertainty: type: standard_deviation; value: 0.03 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench BB-LENGTH-500-DIVERSITY-PAIRWISE-TM: length 500, Diversity pairwise TM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(Native PDBs), column(length 500, Diversity pairwise TM ↓)
Configuration: Native PDBs	Task: ProteinBench BB-LENGTH-500-QUALITY-SCRMSD: length 500, Quality scRMSD Dataset subset: Designed backbones at fixed lengths (ProteinBench split)	1.07 ± 5.96 scrmsd score · lower Uncertainty: type: standard_deviation; value: 5.96 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench BB-LENGTH-500-QUALITY-SCRMSD: length 500, Quality scRMSD Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(Native PDBs), column(length 500, Quality scRMSD ↓)
Configuration: Native PDBs	Task: ProteinBench BB-LENGTH-500-QUALITY-SCTM: length 500, Quality scTM Dataset subset: Designed backbones at fixed lengths (ProteinBench split)	0.97 ± 0.17 sctm score · higher Uncertainty: type: standard_deviation; value: 0.17 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench BB-LENGTH-500-QUALITY-SCTM: length 500, Quality scTM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(Native PDBs), column(length 500, Quality scTM ↑)
Configuration: Native PDBs	Task: ProteinBench CO-LENGTH-100-DIVERSITY-MAX-CLUST: length 100, Diversity Max Clust. Dataset subset: Co-generated structures and sequences at fixed lengths (ProteinBench split)	0.75 max-clust score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench CO-LENGTH-100-DIVERSITY-MAX-CLUST: length 100, Diversity Max Clust. Joint structure and sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 5, row(Native PDBs), column(length 100, Diversity Max Clust. ↑)
Configuration: Native PDBs	Task: ProteinBench CO-LENGTH-100-QUALITY-SCRMSD: length 100, Quality scRMSD Dataset subset: Co-generated structures and sequences at fixed lengths (ProteinBench split)	2.98 ± 3.49 scrmsd score · lower Uncertainty: type: standard_deviation; value: 3.49 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench CO-LENGTH-100-QUALITY-SCRMSD: length 100, Quality scRMSD Joint structure and sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 5, row(Native PDBs), column(length 100, Quality scRMSD ↓)
Configuration: Native PDBs	Task: ProteinBench CO-LENGTH-100-QUALITY-SCTM: length 100, Quality scTM Dataset subset: Co-generated structures and sequences at fixed lengths (ProteinBench split)	0.91 ± 0.11 sctm score · higher Uncertainty: type: standard_deviation; value: 0.11 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench CO-LENGTH-100-QUALITY-SCTM: length 100, Quality scTM Joint structure and sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 5, row(Native PDBs), column(length 100, Quality scTM ↑)
Configuration: Native PDBs	Task: ProteinBench CO-LENGTH-200-DIVERSITY-MAX-CLUST: length 200, Diversity Max Clust. Dataset subset: Co-generated structures and sequences at fixed lengths (ProteinBench split)	0.77 max-clust score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench CO-LENGTH-200-DIVERSITY-MAX-CLUST: length 200, Diversity Max Clust. Joint structure and sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 5, row(Native PDBs), column(length 200, Diversity Max Clust. ↑)
Configuration: Native PDBs	Task: ProteinBench CO-LENGTH-200-QUALITY-SCRMSD: length 200, Quality scRMSD Dataset subset: Co-generated structures and sequences at fixed lengths (ProteinBench split)	3.24 ± 3.77 scrmsd score · lower Uncertainty: type: standard_deviation; value: 3.77 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench CO-LENGTH-200-QUALITY-SCRMSD: length 200, Quality scRMSD Joint structure and sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 5, row(Native PDBs), column(length 200, Quality scRMSD ↓)
Configuration: Native PDBs	Task: ProteinBench CO-LENGTH-200-QUALITY-SCTM: length 200, Quality scTM Dataset subset: Co-generated structures and sequences at fixed lengths (ProteinBench split)	0.88 ± 0.09 sctm score · higher Uncertainty: type: standard_deviation; value: 0.09 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench CO-LENGTH-200-QUALITY-SCTM: length 200, Quality scTM Joint structure and sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 5, row(Native PDBs), column(length 200, Quality scTM ↑)
Configuration: Native PDBs	Task: ProteinBench CO-LENGTH-300-DIVERSITY-MAX-CLUST: length 300, Diversity Max Clust. Dataset subset: Co-generated structures and sequences at fixed lengths (ProteinBench split)	0.75 max-clust score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench CO-LENGTH-300-DIVERSITY-MAX-CLUST: length 300, Diversity Max Clust. Joint structure and sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 5, row(Native PDBs), column(length 300, Diversity Max Clust. ↑)
Configuration: Native PDBs	Task: ProteinBench CO-LENGTH-300-QUALITY-SCRMSD: length 300, Quality scRMSD Dataset subset: Co-generated structures and sequences at fixed lengths (ProteinBench split)	3.94 ± 4.95 scrmsd score · lower Uncertainty: type: standard_deviation; value: 4.95 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench CO-LENGTH-300-QUALITY-SCRMSD: length 300, Quality scRMSD Joint structure and sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 5, row(Native PDBs), column(length 300, Quality scRMSD ↓)
Configuration: Native PDBs	Task: ProteinBench CO-LENGTH-300-QUALITY-SCTM: length 300, Quality scTM Dataset subset: Co-generated structures and sequences at fixed lengths (ProteinBench split)	0.92 ± 0.12 sctm score · higher Uncertainty: type: standard_deviation; value: 0.12 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native PDBs on ProteinBench CO-LENGTH-300-QUALITY-SCTM: length 300, Quality scTM Joint structure and sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 5, row(Native PDBs), column(length 300, Quality scTM ↑)

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