Pairwise alignment score (indel baseline)
Scores an in-frame indel by the global alignment score between the wild-type and mutated protein sequences (match 2, mismatch -1); lower similarity means more likely damaging.
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1 evaluation · 1 result. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Method: Pairwise alignment score (indel baseline) | Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset: ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023) | 0.586 AUROC (ROC-AUC, pathogenic versus benign ClinVar all in-frame indels; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAlignment on all in-frame indels (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_indels' cell B6, row 'Alignment', column 'AUC_indels' |
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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
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- Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) · Original source · Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10)
Technical metadata and extraction receipts
Stable ID: gfm-guides-20261014-esm1b-method-pairwise-alignment-score
- areas
- protein-function
- contexts
- clinical_research
- method types
- conventional_pipeline
- reported name
- Alignment
- entity level
- method
- source locator
- Methods 'Baseline scores of indel and stop-gain variant effects'
- missing metadata
- version: reason: inapplicable; note: Baseline defined in the article's Methods