ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME)

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Evaluations and results

8 evaluations · 8 results. Different protocols are not a single leaderboard.

Dataset: SARS-CoV-2 RBD mutant binding and expression measurements

Sorted by R² (ACE2 binding; Position-stratified split holding out whole mutated positions; the mean over residue embeddings, frozen) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	R² (ACE2 binding; Position-stratified split holding out whole mutated positions; the mean over residue embeddings, frozen)	R² (ACE2 binding; Random split over RBD mutants; the mean over residue embeddings, frozen)	R² (RBD expression; Position-stratified split holding out whole mutated positions; the mean over residue embeddings, frozen)	R² (RBD expression; Random split over RBD mutants; the mean over residue embeddings, frozen)	RMSE (ACE2 binding; Position-stratified split holding out whole mutated positions; the mean over residue embeddings, frozen)	RMSE (ACE2 binding; Random split over RBD mutants; the mean over residue embeddings, frozen)	RMSE (RBD expression; Position-stratified split holding out whole mutated positions; the mean over residue embeddings, frozen)	RMSE (RBD expression; Random split over RBD mutants; the mean over residue embeddings, frozen)
ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME)Evaluation	PRIME ACE2 binding regression, Position-stratified split holding out whole mutated positions, R²	-0.0865 ± 0.04	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME)Evaluation	PRIME ACE2 binding regression, Position-stratified split holding out whole mutated positions, RMSE	Not reported	Not reported	Not reported	Not reported	1.8488 ± 0.03	Not reported	Not reported	Not reported
ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME)Evaluation	PRIME RBD expression regression, Position-stratified split holding out whole mutated positions, R²	Not reported	Not reported	-0.0103 ± 0.03	Not reported	Not reported	Not reported	Not reported	Not reported
ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME)Evaluation	PRIME RBD expression regression, Position-stratified split holding out whole mutated positions, RMSE	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	1.0807 ± 0.01	Not reported
ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME)Evaluation	PRIME ACE2 binding regression, Random split over RBD mutants, R²	Not reported	0.7981 ± 0.13	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME)Evaluation	PRIME ACE2 binding regression, Random split over RBD mutants, RMSE	Not reported	Not reported	Not reported	Not reported	Not reported	0.8091 ± 0.28	Not reported	Not reported
ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME)Evaluation	PRIME RBD expression regression, Random split over RBD mutants, R²	Not reported	Not reported	Not reported	0.7337 ± 0.15	Not reported	Not reported	Not reported	Not reported
ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME)Evaluation	PRIME RBD expression regression, Random split over RBD mutants, RMSE	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.4942 ± 0.14

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME)	Protocol: PRIME ACE2 binding regression, Position-stratified split holding out whole mutated positions, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements	-0.0865 ± 0.04 R² (ACE2 binding; Position-stratified split holding out whole mutated positions; the mean over residue embeddings, frozen) unitless · higher Uncertainty: SD 0.04 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-2 650M Mean frozen: ACE2 binding R², Position-stratified split holding out whole mutated positions lit-protein-20261011-prime-protocol-position-stratified-binding-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 650M' / 'Mean' / '×', columns 'Position-Stratified Split' / 'Binding' / 'R²'
Configuration: ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME)	Protocol: PRIME ACE2 binding regression, Position-stratified split holding out whole mutated positions, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements	1.8488 ± 0.03 RMSE (ACE2 binding; Position-stratified split holding out whole mutated positions; the mean over residue embeddings, frozen) unit-unreported · lower Uncertainty: SD 0.03 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-2 650M Mean frozen: ACE2 binding RMSE, Position-stratified split holding out whole mutated positions lit-protein-20261011-prime-protocol-position-stratified-binding-rmse Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 650M' / 'Mean' / '×', columns 'Position-Stratified Split' / 'Binding' / 'RMSE'
Configuration: ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME)	Protocol: PRIME RBD expression regression, Position-stratified split holding out whole mutated positions, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements	-0.0103 ± 0.03 R² (RBD expression; Position-stratified split holding out whole mutated positions; the mean over residue embeddings, frozen) unitless · higher Uncertainty: SD 0.03 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-2 650M Mean frozen: RBD expression R², Position-stratified split holding out whole mutated positions lit-protein-20261011-prime-protocol-position-stratified-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 650M' / 'Mean' / '×', columns 'Position-Stratified Split' / 'Expression' / 'R²'
Configuration: ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME)	Protocol: PRIME RBD expression regression, Position-stratified split holding out whole mutated positions, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements	1.0807 ± 0.01 RMSE (RBD expression; Position-stratified split holding out whole mutated positions; the mean over residue embeddings, frozen) unit-unreported · lower Uncertainty: SD 0.01 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-2 650M Mean frozen: RBD expression RMSE, Position-stratified split holding out whole mutated positions lit-protein-20261011-prime-protocol-position-stratified-expression-rmse Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 650M' / 'Mean' / '×', columns 'Position-Stratified Split' / 'Expression' / 'RMSE'
Configuration: ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME)	Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements	0.7981 ± 0.13 R² (ACE2 binding; Random split over RBD mutants; the mean over residue embeddings, frozen) unitless · higher Uncertainty: SD 0.13 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-2 650M Mean frozen: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 650M' / 'Mean' / '×', columns 'Random Split' / 'Binding' / 'R²'
Configuration: ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME)	Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements	0.8091 ± 0.28 RMSE (ACE2 binding; Random split over RBD mutants; the mean over residue embeddings, frozen) unit-unreported · lower Uncertainty: SD 0.28 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-2 650M Mean frozen: ACE2 binding RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-rmse Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 650M' / 'Mean' / '×', columns 'Random Split' / 'Binding' / 'RMSE'
Configuration: ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME)	Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements	0.7337 ± 0.15 R² (RBD expression; Random split over RBD mutants; the mean over residue embeddings, frozen) unitless · higher Uncertainty: SD 0.15 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-2 650M Mean frozen: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 650M' / 'Mean' / '×', columns 'Random Split' / 'Expression' / 'R²'
Configuration: ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME)	Protocol: PRIME RBD expression regression, Random split over RBD mutants, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements	0.4942 ± 0.14 RMSE (RBD expression; Random split over RBD mutants; the mean over residue embeddings, frozen) unit-unreported · lower Uncertainty: SD 0.14 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-2 650M Mean frozen: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 650M' / 'Mean' / '×', columns 'Random Split' / 'Expression' / 'RMSE'

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PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Original source · Version of record, BMC Genomics 2026 (PMC13425921 JATS full text)

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Technical metadata and extraction receipts

Stable ID: lit-protein-20261011-prime-config-esm-2-650m-mean-frozen

areas: protein-function
contexts: research
method types: foundation_model
reported name: ESM-2 650M
version: ESM-2 650M
representation: the mean over residue embeddings
training setting: None; frozen representations
foundation model eligible: true
source locator: Table 1, row 'ESM-2 650M' / 'Mean' / '×'

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