Protocol

Methyltransferase dataset stability ranking, Spearman correlation (Chu et al. 2024 Table 1)

Spearman correlation between predicted and measured values for seven methods on Methyltransferase dataset.

Overview

Spearman correlation between predicted and measured values for seven methods on Methyltransferase dataset.

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7 recorded evaluations, 7 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

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All evaluations

7 evaluations · 7 results. 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: ELASPIC-2 (Chu et al. 2024)	Protocol: Methyltransferase dataset stability ranking, Spearman correlation (Chu et al. 2024 Table 1) Dataset: Methyltransferase dataset: Thiopurine S-methyltransferase, protein abundance	0.58 spearman-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ELASPIC-2 on Methyltransferase dataset (Chu et al. 2024) protein-stability-20261009-protocol-chu2024-methyltransferase Aggregation: Not reported Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset · Table 1, row 'Methyltransferase dataset', column 'ELASPIC-2' (supervised group)
Configuration: ESM-2 (35M) (Chu et al. 2024)	Protocol: Methyltransferase dataset stability ranking, Spearman correlation (Chu et al. 2024 Table 1) Dataset: Methyltransferase dataset: Thiopurine S-methyltransferase, protein abundance	0.42 spearman-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ESM-2 (35M) on Methyltransferase dataset (Chu et al. 2024) protein-stability-20261009-protocol-chu2024-methyltransferase Aggregation: Not reported Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset · Table 1, row 'Methyltransferase dataset', column 'ESM-2 (35M)' (unsupervised group)
Configuration: ESM-2 (3B) (Chu et al. 2024)	Protocol: Methyltransferase dataset stability ranking, Spearman correlation (Chu et al. 2024 Table 1) Dataset: Methyltransferase dataset: Thiopurine S-methyltransferase, protein abundance	0.46 spearman-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ESM-2 (3B) on Methyltransferase dataset (Chu et al. 2024) protein-stability-20261009-protocol-chu2024-methyltransferase Aggregation: Not reported Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset · Table 1, row 'Methyltransferase dataset', column 'ESM-2 (3B)' (unsupervised group)
Configuration: ESM therm (Chu et al. 2024)	Protocol: Methyltransferase dataset stability ranking, Spearman correlation (Chu et al. 2024 Table 1) Dataset: Methyltransferase dataset: Thiopurine S-methyltransferase, protein abundance	0.03 spearman-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM therm on Methyltransferase dataset (Chu et al. 2024) protein-stability-20261009-protocol-chu2024-methyltransferase Aggregation: Not reported Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset · Table 1, row 'Methyltransferase dataset', column 'ESMtherm' (supervised group)
Configuration: MUPro (Chu et al. 2024)	Protocol: Methyltransferase dataset stability ranking, Spearman correlation (Chu et al. 2024 Table 1) Dataset: Methyltransferase dataset: Thiopurine S-methyltransferase, protein abundance	0.21 spearman-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MUPro on Methyltransferase dataset (Chu et al. 2024) protein-stability-20261009-protocol-chu2024-methyltransferase Aggregation: Not reported Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset · Table 1, row 'Methyltransferase dataset', column 'MUPro' (supervised group)
Configuration: RaSP (Chu et al. 2024)	Protocol: Methyltransferase dataset stability ranking, Spearman correlation (Chu et al. 2024 Table 1) Dataset: Methyltransferase dataset: Thiopurine S-methyltransferase, protein abundance	0.4 spearman-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RaSP on Methyltransferase dataset (Chu et al. 2024) protein-stability-20261009-protocol-chu2024-methyltransferase Aggregation: Not reported Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset · Table 1, row 'Methyltransferase dataset', column 'RaSP' (supervised group)
Configuration: Rosetta (Chu et al. 2024)	Protocol: Methyltransferase dataset stability ranking, Spearman correlation (Chu et al. 2024 Table 1) Dataset: Methyltransferase dataset: Thiopurine S-methyltransferase, protein abundance	0.48 spearman-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Rosetta on Methyltransferase dataset (Chu et al. 2024) protein-stability-20261009-protocol-chu2024-methyltransferase Aggregation: Not reported Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset · Table 1, row 'Methyltransferase dataset', column 'Rosetta' (supervised group)

Source checking is not independent reproduction. Release 2026-10-10-7fcc3e48a123.

Methods and evaluation design

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Recorded evaluations

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Baseline coverage

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Author-reported evaluations: 1
External evaluations: 6

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Evidence

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Evidence table

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Sources and history

Release 2026-10-10-7fcc3e48a123 · Record review: source checked

1 source records and release history

Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset · Original source · PLOS Computational Biology 20(7):e1012248, published 2024-07-22; PMC11293664 full-text XML

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Technical metadata and extraction receipts

Stable ID: protein-stability-20261009-protocol-chu2024-methyltransferase

areas: proteins-complexes
contexts: research
protocol: Each method scores the variants and Spearman correlation is computed against the measured protein abundance.
version: Table 1
metric: spearman-correlation
limitations: ESM therm was fine-tuned by the authors of this paper; the other methods were run by them as comparators.; Only Spearman correlation is printed; no RMSE, calibration or uncertainty.; The larger-protein benchmark was limited to six ProteinGym datasets and BglB because of Rosetta's compute cost (Methods P25).; Single protein (Thiopurine S-methyltransferase, 245 residues); the measured quantity is protein abundance, not ddG of folding.; ESM therm was fine-tuned on domains of at most 72 residues, so this is an out-of-range test for it.
source locator: Table 1, row 'Methyltransferase dataset'; Table 2

Related records

uses data: Methyltransferase dataset: Thiopurine S-methyltransferase, protein abundance
assessment: ELASPIC-2 on Methyltransferase dataset (Chu et al. 2024)
assessment: ESM-2 (35M) on Methyltransferase dataset (Chu et al. 2024)
assessment: ESM-2 (3B) on Methyltransferase dataset (Chu et al. 2024)
assessment: ESM therm on Methyltransferase dataset (Chu et al. 2024)
assessment: MUPro on Methyltransferase dataset (Chu et al. 2024)
assessment: RaSP on Methyltransferase dataset (Chu et al. 2024)
assessment: Rosetta on Methyltransferase dataset (Chu et al. 2024)
assessed by: Assess methods for protein stability experiments

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