CATH superfamily annotation evaluates protein-domain classification with stringent sequence-identity separation.
Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | CATHe-derived large and small superfamily datasets based on CATH v4.3 and CATH-Gene3D.SourcesCATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets · Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages |
| Splits | Training, validation and test domain sets are retained from CATHe where structural-token availability permits.SourcesCATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets · Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages |
| Metrics | F1 is emphasized for class imbalance; balanced accuracy and MCC are also computed.SourcesCATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets · Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages |
| Baselines | CATHe and alternative embeddings from ProtT5, ProstT5, ESM2, Ankh and TM-Vec; domain availability and input dimensionality differ.SourcesCATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets · Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages |
| Leakage controls | The source reports less than 20% sequence identity within and between the original partitions.SourcesCATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets · Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages |
| Uncertainty | Bootstrap resampling of the test set supplies interval estimates.SourcesCATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets · Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages |
| Entity type | Paper-specific computational evaluation protocol.SourcesCATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets · Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages |
| Organisms | The benchmark spans CATH superfamilies using PDB and AlphaFold-database domains. Data and datasets specifies structural-domain and superfamily coverage, but does not provide a species inventory; superfamily classes are not organism labels. · Not reported in inspected sourcesSourcesCATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets · Data and datasets; 3Di processing |
| Assays | CATH domain superfamily annotations and structural-alphabet representations.SourcesCATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets · Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages |
| Allowed inputs | Amino-acid embeddings, 3Di embeddings, or their concatenation.SourcesCATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets · Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages |
| Adaptation | Frozen protein-model embeddings feed a supervised feed-forward classifier; classifier/data-filter hyperparameters are selected in the study.SourcesCATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets · Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages |
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
CATHe-derived large and small superfamily datasets based on CATH v4.3 and CATH-Gene3D. Training, validation and test domain sets are retained from CATHe where structural-token availability permits. F1 is emphasized for class imbalance; balanced accuracy and MCC are also computed. CATHe and alternative embeddings from ProtT5, ProstT5, ESM2, Ankh and TM-Vec; domain availability and input dimensionality differ. The source reports less than 20% sequence identity within and between the original partitions. Bootstrap resampling of the test set supplies interval estimates.
Each evaluation records what was tested and under which conditions.
Release 2026-09-17-d277315f7d76 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| CATHe2 + ProstT5: CATH superfamily annotation amino-acid and structural alphabet embedding classifier Author-reported evaluation · Evaluation metadata: needs review | ||
| 82.3% F1 Unit: percent · Direction: unknown | Uncertainty: ± 1.3 percentage points Scored: Not reported · Eligible: Not reported | source checkedCATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets · Table 3, ProstT5 full row, F1 score column Source checking is not independent reproduction. |
Last literature check: 2026-09-17. Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
| Paper or primary resource | Version | Reference |
|---|---|---|
| CATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets | journal full text in PMC | Read source |
primary comparison tables located
Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged.
Stable record: reported-task-c98e91ffc7247dTrace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims | CATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Input: Amino-acid embeddings, 3Di embeddings, or their concatenation.","Evaluation: Frozen protein-model embeddings feed a supervised feed-forward classifier; classifier/data-filter hyperparameters are selected in the study.","Readout: F1 is emphasized for class imbalance; balanced accuracy and MCC are also computed."] Individual claims | CATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | CATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets CATHe-derived large and small superfamily datasets based on CATH v4.3 and CATH-Gene3D. Individual claims | CATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits Training, validation and test domain sets are retained from CATHe where structural-token availability permits. Individual claims | CATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Frozen protein-model embeddings feed a supervised feed-forward classifier; classifier/data-filter hyperparameters are selected in the study. Individual claims | CATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics F1 is emphasized for class imbalance; balanced accuracy and MCC are also computed. Individual claims | CATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines CATHe and alternative embeddings from ProtT5, ProstT5, ESM2, Ankh and TM-Vec; domain availability and input dimensionality differ. Individual claims | CATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls The source reports less than 20% sequence identity within and between the original partitions. Individual claims | CATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Uncertainty Bootstrap resampling of the test set supplies interval estimates. Individual claims | CATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets Methods: Data and datasets; Results; cached text lines 11–14, 30; comparative evaluation and ablation passages Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-09-17-d277315f7d76 · Record review: needs review
Stable ID: reported-task-c98e91ffc7247d