Model

ESM-1v

ESM-1v provides protein language models intended for zero-shot variant-effect scoring.

Sources (2)

facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models

5 evaluations · 43 results 1 configuration with further results

How it worksESM-1v workflow

Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.

Sources (2)

facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models

Overview

Model type

Protein transformer for variant-effect scoring

Inputs

Protein amino-acid sequence and the specified sequence variation.

Outputs

Token probabilities used to calculate sequence-variant scores.

Access

Official project documentation and implementation: https://github.com/facebookresearch/esm

Sources (2)

facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models

limited source coverage · Automated source review, 2026-09-16. All specifications and missing details

Evaluations and results

5 evaluations · 43 results. Different protocols are not a single leaderboard.

Sorted by Spearman (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	Spearman	Spearman (ProteinGym zero-shot DMS substitutions, Activity assays: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Binding assays: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Expression assays: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, High MSA depth proteins: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Human proteins: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Low MSA depth proteins: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, mean over selection types of the per-type mean over proteins of assay-level Spearman (all 217 assays))	Spearman (ProteinGym zero-shot DMS substitutions, Medium MSA depth proteins: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Organismal fitness assays: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Other eukaryote proteins: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Prokaryote proteins: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Stability assays: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, variants with 1 substitution: mean over protein and selection-type groups of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, variants with 2 substitutions: mean over protein and selection-type groups of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, variants with 3 substitutions: mean over protein and selection-type groups of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, variants with 4 substitutions: mean over protein and selection-type groups of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, variants with 5 or more substitutions: mean over protein and selection-type groups of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Virus proteins: mean over proteins of assay-level Spearman)	AUROC	MCC	NDCG at 10%	Top 10% recall
ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]Evaluation	ProteinGym AMFR official zero-shot Spearman snapshot, ProteinGym AMFR 4G3O official snapshot cohort	0.423 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
ESM-1v (ensemble)Evaluation	ProteinGym ZS-SUB-SPEARMAN: Zero-shot substitutions, Spearman, ProteinGym substitution DMS assays (ProteinGym split)	0.407	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
ESM-1v (single) [ProteinGym 144fe22b snapshot]Evaluation	ProteinGym AMFR official zero-shot Spearman snapshot, ProteinGym AMFR 4G3O official snapshot cohort	0.07	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
ESM-1v (ensemble)Evaluation	ProteinGym ZS-SUB-AUC: Zero-shot substitutions, AUC, ProteinGym substitution DMS assays (ProteinGym split)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.723	Not reported	Not reported	Not reported
ESM-1v (ensemble)Evaluation	ProteinGym ZS-SUB-MCC: Zero-shot substitutions, MCC, ProteinGym substitution DMS assays (ProteinGym split)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.32	Not reported	Not reported
ESM-1v (ensemble)Evaluation	ProteinGym ZS-SUB-NDCG: Zero-shot substitutions, NDCG@10%, ProteinGym substitution DMS assays (ProteinGym split)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.749	Not reported
ESM-1v (ensemble)Evaluation	ProteinGym ZS-SUB-RECALL: Zero-shot substitutions, top 10% recall, ProteinGym substitution DMS assays (ProteinGym split)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.211
ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]Evaluation	ProteinGym v1.3 zero-shot DMS substitutions, ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	Not reported	0.42 (best in column)	0.32 (best in column)	0.429 (best in column)	0.495 (best in column)	0.458 (best in column)	0.316 (best in column)	0.407 (best in column)	0.409 (best in column)	0.386 (best in column)	0.464 (best in column)	0.413 (best in column)	0.477 (best in column)	0.403 (best in column)	0.215 (best in column)	0.173	0.153 (best in column)	0.218 (best in column)	0.294 (best in column)	Not reported	Not reported	Not reported	Not reported
ESM-1v (single) [ProteinGym 144fe22b snapshot]Evaluation	ProteinGym v1.3 zero-shot DMS substitutions, ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	Not reported	0.396	0.268	0.405	0.47	0.427	0.289	0.374	0.373	0.361	0.433	0.385	0.437	0.375	0.188	0.177 (best in column)	0.146	0.209	0.258	Not reported	Not reported	Not reported	Not reported

All 43 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ESM-1v (ensemble)	Task: ProteinGym ZS-SUB-AUC: Zero-shot substitutions, AUC Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.723 AUROC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ESM-1v (ensemble) on ProteinGym ZS-SUB-AUC: Zero-shot substitutions, AUC Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(ESM-1v (ensemble)), column(Zero-shot substitutions, AUC)
Configuration: ESM-1v (ensemble)	Task: ProteinGym ZS-SUB-MCC: Zero-shot substitutions, MCC Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.32 MCC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ESM-1v (ensemble) on ProteinGym ZS-SUB-MCC: Zero-shot substitutions, MCC Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(ESM-1v (ensemble)), column(Zero-shot substitutions, MCC)
Configuration: ESM-1v (ensemble)	Task: ProteinGym ZS-SUB-NDCG: Zero-shot substitutions, NDCG@10% Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.749 NDCG at 10% unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ESM-1v (ensemble) on ProteinGym ZS-SUB-NDCG: Zero-shot substitutions, NDCG@10% Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(ESM-1v (ensemble)), column(Zero-shot substitutions, NDCG@10%)
Configuration: ESM-1v (ensemble)	Task: ProteinGym ZS-SUB-RECALL: Zero-shot substitutions, top 10% recall Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.211 Top 10% recall fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ESM-1v (ensemble) on ProteinGym ZS-SUB-RECALL: Zero-shot substitutions, top 10% recall Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(ESM-1v (ensemble)), column(Zero-shot substitutions, top 10% recall)
Configuration: ESM-1v (ensemble)	Task: ProteinGym ZS-SUB-SPEARMAN: Zero-shot substitutions, Spearman Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.407 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ESM-1v (ensemble) on ProteinGym ZS-SUB-SPEARMAN: Zero-shot substitutions, Spearman Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(ESM-1v (ensemble)), column(Zero-shot substitutions, Spearman)
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym AMFR official zero-shot Spearman snapshot Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort	0.423 Spearman unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble) AMFR official snapshot Not reported Aggregation: Not reported ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=ESM-1v (ensemble)
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym AMFR official zero-shot Spearman snapshot Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort	0.07 Spearman unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single) AMFR official snapshot Not reported Aggregation: Not reported ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=ESM-1v (single)
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.407 Spearman (ProteinGym zero-shot DMS substitutions, mean over selection types of the per-type mean over proteins of assay-level Spearman (all 217 assays)) unitless · higher Uncertainty: SE 0.013. From compute_bootstrap_standard_error_functional_categories in performance_DMS_benchmarks.py at 144fe22 (default 10,000 resamples, lines 95-111 and 310-315); not an absolute standard error of the model's own average. Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'Average_Spearman'
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.403 Spearman (ProteinGym zero-shot DMS substitutions, variants with 1 substitution: mean over protein and selection-type groups of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'Depth_1'
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.215 Spearman (ProteinGym zero-shot DMS substitutions, variants with 2 substitutions: mean over protein and selection-type groups of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'Depth_2'
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.173 Spearman (ProteinGym zero-shot DMS substitutions, variants with 3 substitutions: mean over protein and selection-type groups of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'Depth_3'
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.153 Spearman (ProteinGym zero-shot DMS substitutions, variants with 4 substitutions: mean over protein and selection-type groups of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'Depth_4'
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.218 Spearman (ProteinGym zero-shot DMS substitutions, variants with 5 or more substitutions: mean over protein and selection-type groups of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'Depth_5+'
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.42 Spearman (ProteinGym zero-shot DMS substitutions, Activity assays: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'Function_Activity'
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.32 Spearman (ProteinGym zero-shot DMS substitutions, Binding assays: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'Function_Binding'
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.429 Spearman (ProteinGym zero-shot DMS substitutions, Expression assays: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'Function_Expression'
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.386 Spearman (ProteinGym zero-shot DMS substitutions, Organismal fitness assays: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'Function_OrganismalFitness'
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.477 Spearman (ProteinGym zero-shot DMS substitutions, Stability assays: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'Function_Stability'
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.495 Spearman (ProteinGym zero-shot DMS substitutions, High MSA depth proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'High_MSA_depth'
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.316 Spearman (ProteinGym zero-shot DMS substitutions, Low MSA depth proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'Low_MSA_depth'
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.409 Spearman (ProteinGym zero-shot DMS substitutions, Medium MSA depth proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'Medium_MSA_depth'
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.458 Spearman (ProteinGym zero-shot DMS substitutions, Human proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'Taxa_Human'
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.464 Spearman (ProteinGym zero-shot DMS substitutions, Other eukaryote proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'Taxa_Other_Eukaryote'
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.413 Spearman (ProteinGym zero-shot DMS substitutions, Prokaryote proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'Taxa_Prokaryote'
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.294 Spearman (ProteinGym zero-shot DMS substitutions, Virus proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (ensemble): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 48, row 'ESM-1v (ensemble)', column 'Taxa_Virus'

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

Further results on linked records

One linked record has results that are not included above, because no reviewed claim yet ties the link to this model. Each record keeps its own settings and evaluations, and its scores are on its own page.

ESM-1v (Livesey and Marsh 2025) Configuration · configuration · 6 evaluations · 7 results

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How it works, versions and access

Versions and evaluated configurations

ESM-1v (ensemble) · family
ESM-1v (ensemble) [ProteinGym 144fe22b snapshot] · configuration of
ESM-1v (single) [ProteinGym 144fe22b snapshot] · configuration of

How it works

Transformer architecture shared with ESM-1b, trained on UniRef90; multiple released model instances support the variant-scoring workflow. The documented inputs are protein amino-acid sequence and the specified sequence variation. The output consists of token probabilities used to calculate sequence-variant scores.

Sources (2)

facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models

Versions and reproducibility

esm1v_t33_650M_UR90S_1 through _5. The applicable input limits require configuration-specific checking.

Sources (2)

facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

The package provides a dedicated variant-prediction example without fitting a task-specific supervised classifier.
Sources (2)
facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models

Limitations and conditions

The five released instances are distinct models. A language-model score is not a calibrated clinical pathogenicity probability.
Sources (2)
facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models

Profile review details

Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied.

Stable record: discovery-model-esm-1v

Specifications

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Inputs, outputs and configuration
Property	Description and evidence
Model type	Protein transformer for variant-effect scoring Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Architecture	Transformer architecture shared with ESM-1b, trained on UniRef90; multiple released model instances support the variant-scoring workflow. Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Inputs	Protein amino-acid sequence and the specified sequence variation. Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Outputs	Token probabilities used to calculate sequence-variant scores. Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Parameters	650 million per model; 33 transformer layers. Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Known versions	esm1v_t33_650M_UR90S_1 through _5. Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Training data	UniRef90/S 2020_03, as reported in the pretrained-model table. Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Training cutoff	The official model table identifies the UniRef90/S2020_03 training release; this is a corpus version rather than a verified latest-sequence deposition date. Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Context limits	The inspected official esm1v_t33_650M_UR90S_1 config reserves 1,026 absolute positions. This includes model positions and is not a claim of 1,026-residue validated biological context. Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Weights licence	Separate checkpoint-distribution terms are not stated in the inspected release documentation and licence material. The source-code licence alone is not recorded as an explicit weight grant. · Not reported in inspected sources Sources (3) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json; facebookresearch/esm: LICENSE · README.md: Main models, Zero-shot variant prediction and Pre-trained Models; LICENSE: licence text
Access	Official project documentation and implementation: https://github.com/facebookresearch/esm Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Code licence	MIT Sources facebookresearch/esm: LICENSE · LICENSE: licence text

Applicable tests and references

Applicability is distinct from a completed evaluation.

ProteinGym · Proposed association

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

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.

40 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	facebook/esm1v_t33_650M_UR90S_1: config.json Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8bfdb1892536cc77bd0760b9c25ddced2cd0b4c8 Retrieved: 2026-09-16T20:12:20.912868+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `6c4b576e2e73ad85fc51a4fa75d4e350532b773e04551307a74643c3fc3c5d59` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	facebookresearch/esm: README.md Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2b369911bb5b4b0dda914521b9475cad1656b2ac Retrieved: 2026-09-16T19:46:19.090082+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `8b273c21a322fc9473d1b68d0dd40c8166ab2f89e4a190aa26ca87251b97cba9` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps Reference protein sequence ESM-1v token predictions Specified variant scoring rule Variant score Individual claims	facebook/esm1v_t33_650M_UR90S_1: config.json Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8bfdb1892536cc77bd0760b9c25ddced2cd0b4c8 Retrieved: 2026-09-16T20:12:20.912868+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `6c4b576e2e73ad85fc51a4fa75d4e350532b773e04551307a74643c3fc3c5d59` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps Reference protein sequence ESM-1v token predictions Specified variant scoring rule Variant score Individual claims	facebookresearch/esm: README.md Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2b369911bb5b4b0dda914521b9475cad1656b2ac Retrieved: 2026-09-16T19:46:19.090082+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `8b273c21a322fc9473d1b68d0dd40c8166ab2f89e4a190aa26ca87251b97cba9` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title ESM-1v workflow Individual claims	facebook/esm1v_t33_650M_UR90S_1: config.json Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8bfdb1892536cc77bd0760b9c25ddced2cd0b4c8 Retrieved: 2026-09-16T20:12:20.912868+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `6c4b576e2e73ad85fc51a4fa75d4e350532b773e04551307a74643c3fc3c5d59` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title ESM-1v workflow Individual claims	facebookresearch/esm: README.md Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2b369911bb5b4b0dda914521b9475cad1656b2ac Retrieved: 2026-09-16T19:46:19.090082+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `8b273c21a322fc9473d1b68d0dd40c8166ab2f89e4a190aa26ca87251b97cba9` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Model type Protein transformer for variant-effect scoring Individual claims	facebook/esm1v_t33_650M_UR90S_1: config.json Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8bfdb1892536cc77bd0760b9c25ddced2cd0b4c8 Retrieved: 2026-09-16T20:12:20.912868+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `6c4b576e2e73ad85fc51a4fa75d4e350532b773e04551307a74643c3fc3c5d59` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Model type Protein transformer for variant-effect scoring Individual claims	facebookresearch/esm: README.md Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2b369911bb5b4b0dda914521b9475cad1656b2ac Retrieved: 2026-09-16T19:46:19.090082+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `8b273c21a322fc9473d1b68d0dd40c8166ab2f89e4a190aa26ca87251b97cba9` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Architecture Transformer architecture shared with ESM-1b, trained on UniRef90; multiple released model instances support the variant-scoring workflow. Individual claims	facebook/esm1v_t33_650M_UR90S_1: config.json Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8bfdb1892536cc77bd0760b9c25ddced2cd0b4c8 Retrieved: 2026-09-16T20:12:20.912868+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `6c4b576e2e73ad85fc51a4fa75d4e350532b773e04551307a74643c3fc3c5d59` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Architecture Transformer architecture shared with ESM-1b, trained on UniRef90; multiple released model instances support the variant-scoring workflow. Individual claims	facebookresearch/esm: README.md Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2b369911bb5b4b0dda914521b9475cad1656b2ac Retrieved: 2026-09-16T19:46:19.090082+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `8b273c21a322fc9473d1b68d0dd40c8166ab2f89e4a190aa26ca87251b97cba9` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: discovered

4 source records and release history

facebookresearch/esm official source · Original source · 2b369911bb5b4b0dda914521b9475cad1656b2ac
facebookresearch/esm: README.md · Original source · 2b369911bb5b4b0dda914521b9475cad1656b2ac
facebook/esm1v_t33_650M_UR90S_1: config.json · Original source · 8bfdb1892536cc77bd0760b9c25ddced2cd0b4c8
facebookresearch/esm: LICENSE · Original source · 2b369911bb5b4b0dda914521b9475cad1656b2ac

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: discovery-model-esm-1v

areas: protein-function
access: official_source_linked
candidate benchmark ids: discovery-benchmark-proteingym
entity level: family
reported name: ESM-1v
entity classification: review date: 2026-09-17; rationale: The cited profile describes a named learned biological predictor or representation model/family. Preserve this identity separately from task-specific fitting, individual checkpoints, pipelines and hosted access.; source ids: evidence-official-29d4b229a3aa426a6dfb; evidence-official-137a3a936ffa4673b3d3; source locator: README.md: Main models, Zero-shot variant prediction and Pre-trained Models; ambiguities: None recorded
missing metadata: version: reason: unextracted

Related records

applicable to: ProteinGym
uses model: ESM-1v (mean)
uses model: ESM-1v (mut mean)
uses model: ESM-1v (per AA)
uses model: Embed. ESM-1v
family: ESM-1v (ensemble)
uses model: OHE ESM-1v
configuration of: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]
configuration of: ESM-1v (single) [ProteinGym 144fe22b snapshot]
configuration of: ESM-1v (Livesey and Marsh 2025)

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