Evaluation

mCSM on S669 (Pancotti et al. 2022)

Published stability-change predictor comparison; transcribed, not reproduced.

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Evaluation results

1 evaluation · 11 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: mCSM (Pancotti et al. 2022)	Protocol: S669 direct and reverse ddG prediction (Pancotti et al. 2022 Table 1) Dataset: S669: 669 single-point variants from ThermoMutDB in proteins under 25% identity to S2648 and VariBench, with reverse variants	–0.05 pearson-correlation unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source mCSM on S669 (Pancotti et al. 2022) protein-stability-20261009-protocol-pancotti2022-s669 Aggregation: Not reported Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset · Table 1, row 'mCSM', column 'Antisimmetry r(d-r)'
Configuration: mCSM (Pancotti et al. 2022)	Protocol: S669 direct and reverse ddG prediction (Pancotti et al. 2022 Table 1) Dataset: S669: 669 single-point variants from ThermoMutDB in proteins under 25% identity to S2648 and VariBench, with reverse variants	–0.85 antisymmetry-bias kilocalorie-per-mole · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source mCSM on S669 (Pancotti et al. 2022) protein-stability-20261009-protocol-pancotti2022-s669 Aggregation: Not reported Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset · Table 1, row 'mCSM', column 'Bias'
Configuration: mCSM (Pancotti et al. 2022)	Protocol: S669 direct and reverse ddG prediction (Pancotti et al. 2022 Table 1) Dataset: S669: 669 single-point variants from ThermoMutDB in proteins under 25% identity to S2648 and VariBench, with reverse variants	1.13 mean-absolute-error kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source mCSM on S669 (Pancotti et al. 2022) protein-stability-20261009-protocol-pancotti2022-s669 Aggregation: Not reported Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset · Table 1, row 'mCSM', column 'Direct MAE'
Configuration: mCSM (Pancotti et al. 2022)	Protocol: S669 direct and reverse ddG prediction (Pancotti et al. 2022 Table 1) Dataset: S669: 669 single-point variants from ThermoMutDB in proteins under 25% identity to S2648 and VariBench, with reverse variants	0.36 pearson-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 mCSM on S669 (Pancotti et al. 2022) protein-stability-20261009-protocol-pancotti2022-s669 Aggregation: Not reported Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset · Table 1, row 'mCSM', column 'Direct r'
Configuration: mCSM (Pancotti et al. 2022)	Protocol: S669 direct and reverse ddG prediction (Pancotti et al. 2022 Table 1) Dataset: S669: 669 single-point variants from ThermoMutDB in proteins under 25% identity to S2648 and VariBench, with reverse variants	1.54 root-mean-squared-error kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source mCSM on S669 (Pancotti et al. 2022) protein-stability-20261009-protocol-pancotti2022-s669 Aggregation: Not reported Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset · Table 1, row 'mCSM', column 'Direct RMSE'
Configuration: mCSM (Pancotti et al. 2022)	Protocol: S669 direct and reverse ddG prediction (Pancotti et al. 2022 Table 1) Dataset: S669: 669 single-point variants from ThermoMutDB in proteins under 25% identity to S2648 and VariBench, with reverse variants	1.86 mean-absolute-error kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source mCSM on S669 (Pancotti et al. 2022) protein-stability-20261009-protocol-pancotti2022-s669 Aggregation: Not reported Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset · Table 1, row 'mCSM', column 'Reverse MAE'
Configuration: mCSM (Pancotti et al. 2022)	Protocol: S669 direct and reverse ddG prediction (Pancotti et al. 2022 Table 1) Dataset: S669: 669 single-point variants from ThermoMutDB in proteins under 25% identity to S2648 and VariBench, with reverse variants	0.22 pearson-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 mCSM on S669 (Pancotti et al. 2022) protein-stability-20261009-protocol-pancotti2022-s669 Aggregation: Not reported Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset · Table 1, row 'mCSM', column 'Reverse r'
Configuration: mCSM (Pancotti et al. 2022)	Protocol: S669 direct and reverse ddG prediction (Pancotti et al. 2022 Table 1) Dataset: S669: 669 single-point variants from ThermoMutDB in proteins under 25% identity to S2648 and VariBench, with reverse variants	2.3 root-mean-squared-error kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source mCSM on S669 (Pancotti et al. 2022) protein-stability-20261009-protocol-pancotti2022-s669 Aggregation: Not reported Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset · Table 1, row 'mCSM', column 'Reverse RMSE'
Configuration: mCSM (Pancotti et al. 2022)	Protocol: S669 direct and reverse ddG prediction (Pancotti et al. 2022 Table 1) Dataset: S669: 669 single-point variants from ThermoMutDB in proteins under 25% identity to S2648 and VariBench, with reverse variants	1.49 mean-absolute-error kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source mCSM on S669 (Pancotti et al. 2022) protein-stability-20261009-protocol-pancotti2022-s669 Aggregation: Not reported Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset · Table 1, row 'mCSM', column 'Total MAE'
Configuration: mCSM (Pancotti et al. 2022)	Protocol: S669 direct and reverse ddG prediction (Pancotti et al. 2022 Table 1) Dataset: S669: 669 single-point variants from ThermoMutDB in proteins under 25% identity to S2648 and VariBench, with reverse variants	0.37 pearson-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 mCSM on S669 (Pancotti et al. 2022) protein-stability-20261009-protocol-pancotti2022-s669 Aggregation: Not reported Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset · Table 1, row 'mCSM', column 'Total r'
Configuration: mCSM (Pancotti et al. 2022)	Protocol: S669 direct and reverse ddG prediction (Pancotti et al. 2022 Table 1) Dataset: S669: 669 single-point variants from ThermoMutDB in proteins under 25% identity to S2648 and VariBench, with reverse variants	1.96 root-mean-squared-error kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source mCSM on S669 (Pancotti et al. 2022) protein-stability-20261009-protocol-pancotti2022-s669 Aggregation: Not reported Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset · Table 1, row 'mCSM', column 'Total RMSE'

Source checking is not independent reproduction. Release 2026-10-10-6e93f504adfc.

Evaluation procedure

protein-stability-20261009-protocol-pancotti2022-s669

Configuration: mCSM (Pancotti et al. 2022)
Protocol: S669 direct and reverse ddG prediction (Pancotti et al. 2022 Table 1)
Dataset: S669: 669 single-point variants from ThermoMutDB in proteins under 25% identity to S2648 and VariBench, with reverse variants

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-09
protocol id: protein-stability-20261009-protocol-pancotti2022-s669
dataset version: Not reported
split: External test set
population: 669 direct and 669 reverse variants
inputs: Protein sequence or structure and the variant
adaptation: Not reported
metric implementation: Pearson r, RMSE and MAE between predicted and experimental ddG
aggregation: Pooled over variants
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: External test set
Adaptation: Not reported
Scoring implementation: Pearson r, RMSE and MAE between predicted and experimental ddG

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

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Evidence table

Inspect claims, sources and review details

Trace 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.

19 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-10-6e93f504adfc
Property and statement	Original source and location	Review and provenance
attributes.comparison.adaptation Not reported Context-only references	Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset Original source ↗ Table 1, row 'mCSM' Version: Briefings in Bioinformatics 23(2):bbab555, published 2022-01-11; PMC8921618 full-text XML Retrieved: 2026-10-09T21:00:42Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `132038084a57c060add54f152f68a69ccaf198337f86a5ec03d39496945c0024` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation Pooled over variants Context-only references	Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset Original source ↗ Table 1, row 'mCSM' Version: Briefings in Bioinformatics 23(2):bbab555, published 2022-01-11; PMC8921618 full-text XML Retrieved: 2026-10-09T21:00:42Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `132038084a57c060add54f152f68a69ccaf198337f86a5ec03d39496945c0024` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget Not reported Context-only references	Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset Original source ↗ Table 1, row 'mCSM' Version: Briefings in Bioinformatics 23(2):bbab555, published 2022-01-11; PMC8921618 full-text XML Retrieved: 2026-10-09T21:00:42Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `132038084a57c060add54f152f68a69ccaf198337f86a5ec03d39496945c0024` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version Not reported Context-only references	Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset Original source ↗ Table 1, row 'mCSM' Version: Briefings in Bioinformatics 23(2):bbab555, published 2022-01-11; PMC8921618 full-text XML Retrieved: 2026-10-09T21:00:42Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `132038084a57c060add54f152f68a69ccaf198337f86a5ec03d39496945c0024` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.inputs Protein sequence or structure and the variant Context-only references	Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset Original source ↗ Table 1, row 'mCSM' Version: Briefings in Bioinformatics 23(2):bbab555, published 2022-01-11; PMC8921618 full-text XML Retrieved: 2026-10-09T21:00:42Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `132038084a57c060add54f152f68a69ccaf198337f86a5ec03d39496945c0024` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.metric_implementation Pearson r, RMSE and MAE between predicted and experimental ddG Context-only references	Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset Original source ↗ Table 1, row 'mCSM' Version: Briefings in Bioinformatics 23(2):bbab555, published 2022-01-11; PMC8921618 full-text XML Retrieved: 2026-10-09T21:00:42Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `132038084a57c060add54f152f68a69ccaf198337f86a5ec03d39496945c0024` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.population 669 direct and 669 reverse variants Context-only references	Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset Original source ↗ Table 1, row 'mCSM' Version: Briefings in Bioinformatics 23(2):bbab555, published 2022-01-11; PMC8921618 full-text XML Retrieved: 2026-10-09T21:00:42Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `132038084a57c060add54f152f68a69ccaf198337f86a5ec03d39496945c0024` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.protocol_id protein-stability-20261009-protocol-pancotti2022-s669 Context-only references	Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset Original source ↗ Table 1, row 'mCSM' Version: Briefings in Bioinformatics 23(2):bbab555, published 2022-01-11; PMC8921618 full-text XML Retrieved: 2026-10-09T21:00:42Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `132038084a57c060add54f152f68a69ccaf198337f86a5ec03d39496945c0024` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.split External test set Context-only references	Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset Original source ↗ Table 1, row 'mCSM' Version: Briefings in Bioinformatics 23(2):bbab555, published 2022-01-11; PMC8921618 full-text XML Retrieved: 2026-10-09T21:00:42Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `132038084a57c060add54f152f68a69ccaf198337f86a5ec03d39496945c0024` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.limitations 1 values Run with default parameters by Pancotti et al., whose authors develop several of the competing tools (ACDC-NN, DDGun, INPS, I-Mutant). Context-only references	Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset Original source ↗ Table 1, row 'mCSM' Version: Briefings in Bioinformatics 23(2):bbab555, published 2022-01-11; PMC8921618 full-text XML Retrieved: 2026-10-09T21:00:42Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.limitations` Source artifact SHA-256: `132038084a57c060add54f152f68a69ccaf198337f86a5ec03d39496945c0024` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-10-10-6e93f504adfc · Record review: source checked

1 source records and release history

Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset · Original source · Briefings in Bioinformatics 23(2):bbab555, published 2022-01-11; PMC8921618 full-text XML

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Technical metadata and extraction receipts

Stable ID: protein-stability-20261009-eval-pancotti2022-mcsm-s669

areas: proteins-complexes
contexts: research
origin: independent_paper
protocol: protein-stability-20261009-protocol-pancotti2022-s669
version: Primary source as retrieved 2026-10-09
comparison: protocol id: protein-stability-20261009-protocol-pancotti2022-s669; dataset version: Not reported; split: External test set; population: 669 direct and 669 reverse variants; inputs: Protein sequence or structure and the variant; adaptation: Not reported; metric implementation: Pearson r, RMSE and MAE between predicted and experimental ddG; aggregation: Pooled over variants; budget: Not reported
source locator: Table 1, row 'mCSM'
missing metadata: comparison.dataset version: reason: unreported
limitations: Run with default parameters by Pancotti et al., whose authors develop several of the competing tools (ACDC-NN, DDGun, INPS, I-Mutant).

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