ESM1b weighted PLLR indel score (Brandes et al. 2023)
ESM-1b in-frame indel score: the pseudo-log-likelihoods of the mutated and wild-type sequences each divided by sequence length before subtraction, to correct for indel size.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: ESM1b weighted PLLR indel score (Brandes et al. 2023) | 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) | 0.861 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 sourceESM1b-wPLLR 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 B4, row 'ESM1b-wPLLR', column 'AUC_indels' |
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- 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)
- Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · 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-config-esm1b-wpllr
- areas
- protein-function
- contexts
- clinical_research
- method types
- foundation_model
- reported name
- ESM1b-wPLLR
- version
- esm1b_t33_650M_UR50S
- parameters
- esm1b_t33_650M_UR50S; sequences longer than 1,022 amino acids scored on a 1,022-residue window around the variant; PLL(mut)/L(mut) - PLL(WT)/L(WT)
- foundation model eligible
- true
- source locator
- Methods 'Generalized effect scores for indels and stop-gain variants' paragraph 3; Supplementary Table 2 sheet 'Table_of_results_indels' row 'ESM1b-wPLLR'
Related records
- configuration of: ESM-1b
- system: ESM1b-wPLLR on all in-frame indels (Brandes et al. 2023)