Configuration

LIST-S2 [ProteinGym 144fe22 clinical summary]

Configuration of LIST-S2, from the ProteinGym clinical reference scores at commit 144fe22b (dbNSFP 4.4a scores).

Overview

LIST-S2: Quantifies the conservation of a position from local sequence identity and taxonomic distances in a multiple alignment, for sequences from any organism rather than human alone.

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

Evaluations and results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: LIST-S2 [ProteinGym 144fe22 clinical summary]	Protocol: ProteinGym clinical substitutions, zero-shot, average AUC (commit 144fe22) Dataset subset: ProteinGym clinical substitution benchmark at commit 144fe22	0.842 AUROC (ProteinGym clinical substitutions, zero-shot, Average_AUC over proteins) unitless · higher Uncertainty: ± 0.005 (type not stated). Labelled a bootstrap standard error. The script that wrote the clinical summary was not read; in the DMS script the same column is the standard error of the difference from the top model, and the top row here prints 0.0, which suggests the same construction. Not verified for this file. Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source LIST-S2: ProteinGym clinical substitutions, zero-shot, average AUC (commit 144fe22) ProteinGym clinical substitutions, zero-shot, average AUC (commit 144fe22) Aggregation: Not reported ProteinGym clinical zero-shot substitutions AUC summary at commit 144fe22 · benchmarks/clinical_zero_shot/substitutions/AUC/Summary_performance_clinical_substitutions_AUC.csv line 13, row 'LIST-S2', column 'Average_AUC'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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How it works, versions and access

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Evidence

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Evidence table

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

4 source records and release history

ProteinGym clinical zero-shot substitutions AUC summary at commit 144fe22 · Original source · 144fe22b07dfaeec2b366f2346203a9838a55b4c
ProteinGym clinical supervised substitutions AUC summary at commit 144fe22 · Original source · 144fe22b07dfaeec2b366f2346203a9838a55b4c
ProteinGym clinical zero-shot indels AUC summary at commit 144fe22 · Original source · 144fe22b07dfaeec2b366f2346203a9838a55b4c
OATML-Markslab/ProteinGym / README.md · Original source · Git commit 144fe22b07dfaeec2b366f2346203a9838a55b4c

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Technical metadata and extraction receipts

Stable ID: vep-lit-20261014-config-proteingym-clinical-list-s2

areas: proteins-complexes; dna-genomes
contexts: clinical_research
method types: specialist
reported name: LIST-S2
foundation model eligible: false
configuration type: reported_configuration
version: dbNSFP 4.4a scores (README line 106: clinical baselines from dbNSFP 4.4a); ProteinGym commit 144fe22b07dfaeec2b366f2346203a9838a55b4c
access reuse: Scores distributed by ProteinGym (README 'Clinical Model scores' downloads); original tool terms apply
source locator: ProteinGym clinical summary CSVs at 144fe22b07dfaeec2b366f2346203a9838a55b4c, Model_name 'LIST-S2', Model type 'Clinical Predictor'
review: reviewer: claude; reviewer note: Claude review agent; no human review claimed. Independent Claude (Opus 5.5) review agent, separate from the extraction agent that built this batch. Automated review only. Transcription, not reproduction.; reviewed at: 2026-10-14T15:30:00Z; artifact sha256: fbe453d1aaa6c30a1d0adf610f7fc23c36044a8e2548b178d316777383f8fe93; retrieval url: https://raw.githubusercontent.com/OATML-Markslab/ProteinGym/144fe22b07dfaeec2b366f2346203a9838a55b4c/benchmarks/clinical_zero_shot/substitutions/AUC/Summary_performance_clinical_substitutions_AUC.csv; method: ai-assisted-source-review; scope-review; method note: Descriptive fields, identity links and missing-metadata reasons checked against the cited sources.; note: Checked; see the dated review for rulings on identity and method type.
provenance note: LIST-S2 as listed in the ProteinGym clinical benchmark summary at commit 144fe22.

Related records

configuration of: LIST-S2
system: LIST-S2: ProteinGym clinical substitutions, zero-shot, average AUC (commit 144fe22)

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