Native Seqs | configuration

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Evaluations and results

12 evaluations · 12 results. Different protocols are not a single leaderboard.

Dataset subset: Generated sequences at fixed lengths (ProteinBench split)

Sorted by Plddt (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	Plddt	Proteinbench max clust	Proteinbench pairwise TM
Native SeqsEvaluation	ProteinBench SEQ-LENGTH-100-QUALITY-PLDDT: length 100, Quality pLDDT	68.46 ± 16.50 (best in column)	Not reported	Not reported
Native SeqsEvaluation	ProteinBench SEQ-LENGTH-500-QUALITY-PLDDT: length 500, Quality pLDDT	62.95 ± 12.60	Not reported	Not reported
Native SeqsEvaluation	ProteinBench SEQ-LENGTH-200-QUALITY-PLDDT: length 200, Quality pLDDT	61.91 ± 11.62	Not reported	Not reported
Native SeqsEvaluation	ProteinBench SEQ-LENGTH-300-QUALITY-PLDDT: length 300, Quality pLDDT	61.49 ± 14.47	Not reported	Not reported
Native SeqsEvaluation	ProteinBench SEQ-LENGTH-100-DIVERSITY-MAX-CLUST: length 100, Diversity Max Clust.	Not reported	0.75	Not reported
Native SeqsEvaluation	ProteinBench SEQ-LENGTH-100-DIVERSITY-PAIRWISE-TM: length 100, Diversity pairwise TM	Not reported	Not reported	0.55 ± 0.19
Native SeqsEvaluation	ProteinBench SEQ-LENGTH-200-DIVERSITY-MAX-CLUST: length 200, Diversity Max Clust.	Not reported	0.78	Not reported
Native SeqsEvaluation	ProteinBench SEQ-LENGTH-200-DIVERSITY-PAIRWISE-TM: length 200, Diversity pairwise TM	Not reported	Not reported	0.49 ± 0.10 (best in column)
Native SeqsEvaluation	ProteinBench SEQ-LENGTH-300-DIVERSITY-MAX-CLUST: length 300, Diversity Max Clust.	Not reported	0.85 (best in column)	Not reported
Native SeqsEvaluation	ProteinBench SEQ-LENGTH-300-DIVERSITY-PAIRWISE-TM: length 300, Diversity pairwise TM	Not reported	Not reported	0.51 ± 0.13
Native SeqsEvaluation	ProteinBench SEQ-LENGTH-500-DIVERSITY-MAX-CLUST: length 500, Diversity Max Clust.	Not reported	0.78	Not reported
Native SeqsEvaluation	ProteinBench SEQ-LENGTH-500-DIVERSITY-PAIRWISE-TM: length 500, Diversity pairwise TM	Not reported	Not reported	0.51 ± 0.11

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: Native Seqs	Task: ProteinBench SEQ-LENGTH-100-DIVERSITY-MAX-CLUST: length 100, Diversity Max Clust. Dataset subset: Generated sequences at fixed lengths (ProteinBench split)	0.75 Proteinbench max clust fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native Seqs on ProteinBench SEQ-LENGTH-100-DIVERSITY-MAX-CLUST: length 100, Diversity Max Clust. Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(Native Seqs), column(length 100, Diversity Max Clust. ↑)
Configuration: Native Seqs	Task: ProteinBench SEQ-LENGTH-100-DIVERSITY-PAIRWISE-TM: length 100, Diversity pairwise TM Dataset subset: Generated sequences at fixed lengths (ProteinBench split)	0.55 ± 0.19 Proteinbench pairwise TM unitless · lower Uncertainty: SD 0.19 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native Seqs on ProteinBench SEQ-LENGTH-100-DIVERSITY-PAIRWISE-TM: length 100, Diversity pairwise TM Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(Native Seqs), column(length 100, Diversity pairwise TM ↓)
Configuration: Native Seqs	Task: ProteinBench SEQ-LENGTH-100-QUALITY-PLDDT: length 100, Quality pLDDT Dataset subset: Generated sequences at fixed lengths (ProteinBench split)	68.46 ± 16.50 Plddt unitless · higher Uncertainty: SD 16.50 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native Seqs on ProteinBench SEQ-LENGTH-100-QUALITY-PLDDT: length 100, Quality pLDDT Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(Native Seqs), column(length 100, Quality pLDDT ↑)
Configuration: Native Seqs	Task: ProteinBench SEQ-LENGTH-200-DIVERSITY-MAX-CLUST: length 200, Diversity Max Clust. Dataset subset: Generated sequences at fixed lengths (ProteinBench split)	0.78 Proteinbench max clust fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native Seqs on ProteinBench SEQ-LENGTH-200-DIVERSITY-MAX-CLUST: length 200, Diversity Max Clust. Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(Native Seqs), column(length 200, Diversity Max Clust. ↑)
Configuration: Native Seqs	Task: ProteinBench SEQ-LENGTH-200-DIVERSITY-PAIRWISE-TM: length 200, Diversity pairwise TM Dataset subset: Generated sequences at fixed lengths (ProteinBench split)	0.49 ± 0.10 Proteinbench pairwise TM unitless · lower Uncertainty: SD 0.10 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native Seqs on ProteinBench SEQ-LENGTH-200-DIVERSITY-PAIRWISE-TM: length 200, Diversity pairwise TM Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(Native Seqs), column(length 200, Diversity pairwise TM ↓)
Configuration: Native Seqs	Task: ProteinBench SEQ-LENGTH-200-QUALITY-PLDDT: length 200, Quality pLDDT Dataset subset: Generated sequences at fixed lengths (ProteinBench split)	61.91 ± 11.62 Plddt unitless · higher Uncertainty: SD 11.62 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native Seqs on ProteinBench SEQ-LENGTH-200-QUALITY-PLDDT: length 200, Quality pLDDT Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(Native Seqs), column(length 200, Quality pLDDT↑)
Configuration: Native Seqs	Task: ProteinBench SEQ-LENGTH-300-DIVERSITY-MAX-CLUST: length 300, Diversity Max Clust. Dataset subset: Generated sequences at fixed lengths (ProteinBench split)	0.85 Proteinbench max clust fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native Seqs on ProteinBench SEQ-LENGTH-300-DIVERSITY-MAX-CLUST: length 300, Diversity Max Clust. Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(Native Seqs), column(length 300, Diversity Max Clust. ↑)
Configuration: Native Seqs	Task: ProteinBench SEQ-LENGTH-300-DIVERSITY-PAIRWISE-TM: length 300, Diversity pairwise TM Dataset subset: Generated sequences at fixed lengths (ProteinBench split)	0.51 ± 0.13 Proteinbench pairwise TM unitless · lower Uncertainty: SD 0.13 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native Seqs on ProteinBench SEQ-LENGTH-300-DIVERSITY-PAIRWISE-TM: length 300, Diversity pairwise TM Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(Native Seqs), column(length 300, Diversity pairwise TM ↓)
Configuration: Native Seqs	Task: ProteinBench SEQ-LENGTH-300-QUALITY-PLDDT: length 300, Quality pLDDT Dataset subset: Generated sequences at fixed lengths (ProteinBench split)	61.49 ± 14.47 Plddt unitless · higher Uncertainty: SD 14.47 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native Seqs on ProteinBench SEQ-LENGTH-300-QUALITY-PLDDT: length 300, Quality pLDDT Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(Native Seqs), column(length 300, Quality pLDDT ↑)
Configuration: Native Seqs	Task: ProteinBench SEQ-LENGTH-500-DIVERSITY-MAX-CLUST: length 500, Diversity Max Clust. Dataset subset: Generated sequences at fixed lengths (ProteinBench split)	0.78 Proteinbench max clust fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native Seqs on ProteinBench SEQ-LENGTH-500-DIVERSITY-MAX-CLUST: length 500, Diversity Max Clust. Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(Native Seqs), column(length 500, Diversity Max Clust. ↑)
Configuration: Native Seqs	Task: ProteinBench SEQ-LENGTH-500-DIVERSITY-PAIRWISE-TM: length 500, Diversity pairwise TM Dataset subset: Generated sequences at fixed lengths (ProteinBench split)	0.51 ± 0.11 Proteinbench pairwise TM unitless · lower Uncertainty: SD 0.11 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native Seqs on ProteinBench SEQ-LENGTH-500-DIVERSITY-PAIRWISE-TM: length 500, Diversity pairwise TM Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(Native Seqs), column(length 500, Diversity pairwise TM ↓)
Configuration: Native Seqs	Task: ProteinBench SEQ-LENGTH-500-QUALITY-PLDDT: length 500, Quality pLDDT Dataset subset: Generated sequences at fixed lengths (ProteinBench split)	62.95 ± 12.60 Plddt unitless · higher Uncertainty: SD 12.60 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Native Seqs on ProteinBench SEQ-LENGTH-500-QUALITY-PLDDT: length 500, Quality pLDDT Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(Native Seqs), column(length 500, Quality pLDDT↑)

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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proteinbench primary benchmark evidence · Original source · 2409.06744v1

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Technical metadata and extraction receipts

Stable ID: proteinbench-method-native-seqs

areas: proteins-complexes
source locator: Table 4, row(Native Seqs)
missing metadata: checkpoint revision: reason: unreported; parameters: reason: unextracted
provenance note: Protein model evaluated by the ProteinBench authors under their harness.

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