Configuration

ESM3

ESM3 generates and completes protein sequence, structure and functional annotations using a shared multimodal representation.

Sources (3)

evolutionaryscale/esm: README.md; evolutionaryscale/esm: _assets/ESM3_README.md; evolutionaryscale/esm: THIRD_PARTY_NOTICE.md · _assets/ESM3_README.md: overview, ESM3 Family, Running Locally and Licenses

12 evaluations · 12 results

How it worksESM3 workflow

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

Sources (3)

Overview

Model type

Multitrack generative protein transformer

Inputs

Complete or partial protein sequence, structure and function-keyword tracks.

Outputs

Completed sequence, structure and functional tracks.

Access

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

Sources (3)

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

Evaluations and results

12 evaluations · 12 results. Different protocols are not a single leaderboard.

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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: ESM3	Task: PFMBench ANTI-RES: Antibiotic resistance Dataset subset: Antibiotic resistance (PFMBench split)	0.584 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM3 on PFMBench ANTI-RES: Antibiotic resistance Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ESM3 [ 18 ]), column(Anti.Res.)
Configuration: ESM3	Task: PFMBench BINDING-DB: BindingDB Dataset subset: BindingDB (PFMBench split)	0.225 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM3 on PFMBench BINDING-DB: BindingDB Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ESM3 [ 18 ]), column(Bind. DB)
Configuration: ESM3	Task: PFMBench CLONING-CLF: Cloning CLF Dataset subset: Cloning CLF (PFMBench split)	0.774 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM3 on PFMBench CLONING-CLF: Cloning CLF Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ESM3 [ 18 ]), column(Clo. CLF)
Configuration: ESM3	Task: PFMBench DEEPLOC2: DeepLoc2 Multi Dataset subset: DeepLoc2 Multi (PFMBench split)	0.659 f1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM3 on PFMBench DEEPLOC2: DeepLoc2 Multi Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ESM3 [ 18 ]), column(DL2 M.)
Configuration: ESM3	Task: PFMBench DEEPSOL: DeepSol Dataset subset: DeepSol (PFMBench split)	0.781 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM3 on PFMBench DEEPSOL: DeepSol Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ESM3 [ 18 ]), column(DeepSol)
Configuration: ESM3	Task: PFMBench EC: Enzyme Commission Dataset subset: Enzyme Commission (PFMBench split)	0.648 f1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM3 on PFMBench EC: Enzyme Commission Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ESM3 [ 18 ]), column(EC)
Configuration: ESM3	Task: PFMBench MAT-PROD: Material production Dataset subset: Material production (PFMBench split)	0.775 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM3 on PFMBench MAT-PROD: Material production Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ESM3 [ 18 ]), column(Mat.Pro.)
Configuration: ESM3	Task: PFMBench METAL-ION: Metal ion binding Dataset subset: Metal ion binding (PFMBench split)	0.703 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM3 on PFMBench METAL-ION: Metal ion binding Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ESM3 [ 18 ]), column(M. I. Bin.)
Configuration: ESM3	Task: PFMBench PDB-BIND: PDBbind Dataset subset: PDBbind (PFMBench split)	0.156 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM3 on PFMBench PDB-BIND: PDBbind Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ESM3 [ 18 ]), column(PDBBind)
Configuration: ESM3	Task: PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction Dataset subset: ProteinGym (PFMBench split)	0.414 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM3 on PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction Scored zero-shot, with no fine-tuning, as reported in PFMBench Table 4. Aggregation: Not reported pfmbench primary benchmark evidence · Table 4, row(ESM3 [ 18 ]), column(ProteinGym)
Configuration: ESM3	Task: PFMBench SEC-STRUCT: Secondary structure Dataset subset: Secondary structure (PFMBench split)	0.813 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM3 on PFMBench SEC-STRUCT: Secondary structure Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ESM3 [ 18 ]), column(Sec. Str.)
Configuration: ESM3	Task: PFMBench STABILITY: TAPE_Stability Dataset subset: TAPE_Stability (PFMBench split)	0.157 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM3 on PFMBench STABILITY: TAPE_Stability Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ESM3 [ 18 ]), column(Stability)

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

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How it works, versions and access

Related profile: ESM3. This page retains the exact record and its evaluation context.

This configuration

Protein foundation model evaluated by the PFMBench authors under their fine-tuning protocol. Input family: Sequence-Structure-Function.

record: ESM3
configuration: Not reported
entity type: Configuration

How it works

ESM3 generates and completes protein sequence, structure and functional annotations using a shared multimodal representation. Transformer generative masked-language model with discrete sequence, structure and function tracks; generation iteratively fills masked positions. The documented inputs are complete or partial protein sequence, structure and function-keyword tracks. The output consists of completed sequence, structure and functional tracks.

Sources (3)

Versions and reproducibility

Published March 2024 small/medium/large models, August 2024 small/medium models, and esm3-sm-open-v1 local weights. The applicable input limits require configuration-specific checking.

Sources (3)

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

Partial prompts can constrain more than one biological property in the same generation workflow.
Sources (3)
evolutionaryscale/esm: README.md; evolutionaryscale/esm: _assets/ESM3_README.md; evolutionaryscale/esm: THIRD_PARTY_NOTICE.md · _assets/ESM3_README.md: overview, ESM3 Family, Running Locally and Licenses

Limitations and conditions

Open local weights and API model names refer to different released sizes and dates; results require the actual configuration, not only the ESM3 family name.
Sources (3)
evolutionaryscale/esm: README.md; evolutionaryscale/esm: _assets/ESM3_README.md; evolutionaryscale/esm: THIRD_PARTY_NOTICE.md · _assets/ESM3_README.md: overview, ESM3 Family, Running Locally and Licenses

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-esm3

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	Multitrack generative protein transformer Sources (3) evolutionaryscale/esm: README.md; evolutionaryscale/esm: _assets/ESM3_README.md; evolutionaryscale/esm: THIRD_PARTY_NOTICE.md · _assets/ESM3_README.md: overview, ESM3 Family, Running Locally and Licenses
Architecture	Transformer generative masked-language model with discrete sequence, structure and function tracks; generation iteratively fills masked positions. Sources (3) evolutionaryscale/esm: README.md; evolutionaryscale/esm: _assets/ESM3_README.md; evolutionaryscale/esm: THIRD_PARTY_NOTICE.md · _assets/ESM3_README.md: overview, ESM3 Family, Running Locally and Licenses
Inputs	Complete or partial protein sequence, structure and function-keyword tracks. Sources (3) evolutionaryscale/esm: README.md; evolutionaryscale/esm: _assets/ESM3_README.md; evolutionaryscale/esm: THIRD_PARTY_NOTICE.md · _assets/ESM3_README.md: overview, ESM3 Family, Running Locally and Licenses
Outputs	Completed sequence, structure and functional tracks. Sources (3) evolutionaryscale/esm: README.md; evolutionaryscale/esm: _assets/ESM3_README.md; evolutionaryscale/esm: THIRD_PARTY_NOTICE.md · _assets/ESM3_README.md: overview, ESM3 Family, Running Locally and Licenses
Parameters	1.4B small, 7B medium and 98B large variants. Sources (3) evolutionaryscale/esm: README.md; evolutionaryscale/esm: _assets/ESM3_README.md; evolutionaryscale/esm: THIRD_PARTY_NOTICE.md · _assets/ESM3_README.md: overview, ESM3 Family, Running Locally and Licenses
Known versions	Published March 2024 small/medium/large models, August 2024 small/medium models, and esm3-sm-open-v1 local weights. Sources (3) evolutionaryscale/esm: README.md; evolutionaryscale/esm: _assets/ESM3_README.md; evolutionaryscale/esm: THIRD_PARTY_NOTICE.md · _assets/ESM3_README.md: overview, ESM3 Family, Running Locally and Licenses
Training data	ESM3 overview reports 2.78 billion proteins and 771 billion unique tokens for the largest model; this is not a verified per-checkpoint manifest. Sources (3) evolutionaryscale/esm: README.md; evolutionaryscale/esm: _assets/ESM3_README.md; evolutionaryscale/esm: THIRD_PARTY_NOTICE.md · _assets/ESM3_README.md: overview, ESM3 Family, Running Locally and Licenses
Training cutoff	The inspected ESM3 release documentation does not supply one latest-data date shared across its sequence, structure and function tracks. · Not reported in inspected sources Sources (3) evolutionaryscale/esm: README.md; evolutionaryscale/esm: _assets/ESM3_README.md; evolutionaryscale/esm: THIRD_PARTY_NOTICE.md · _assets/ESM3_README.md: overview, ESM3 Family, Running Locally and Licenses
Context limits	The inspected ESM3 family documentation does not establish one context limit for local small, hosted medium and hosted large models; a specific service/checkpoint is required. · Not reported in inspected sources Sources (3) evolutionaryscale/esm: README.md; evolutionaryscale/esm: _assets/ESM3_README.md; evolutionaryscale/esm: THIRD_PARTY_NOTICE.md · _assets/ESM3_README.md: overview, ESM3 Family, Running Locally and Licenses
Weights licence	MIT stated in the inspected ESM3 README; model and API access conditions remain separate. Sources (3) evolutionaryscale/esm: README.md; evolutionaryscale/esm: _assets/ESM3_README.md; evolutionaryscale/esm: THIRD_PARTY_NOTICE.md · _assets/ESM3_README.md: overview, ESM3 Family, Running Locally and Licenses
Access	Official project documentation and implementation: https://github.com/evolutionaryscale/esm Sources (3) evolutionaryscale/esm: README.md; evolutionaryscale/esm: _assets/ESM3_README.md; evolutionaryscale/esm: THIRD_PARTY_NOTICE.md · _assets/ESM3_README.md: overview, ESM3 Family, Running Locally and Licenses
Code licence	MIT Sources evolutionaryscale/esm: LICENSE.md · LICENSE.md: licence text

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.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
Relationship: family discovery-model-esm3 Individual claims	pfmbench primary benchmark evidence Original source ↗ Section 3.3 Supported Models; Table 2 model identity and Table 3 named row Version: 2506.14796v1 Retrieved: 2026-09-16T21:06:29.716004+00:00	source checked automated source review · 2026-09-23 Audit details Source review establishes this relationship only. Exact evaluated configurations and original numerical review status remain unchanged. Source identifies ESM-2 650M, ESM-C 600M and ESM3 as the respective foundation models evaluated with adapter tuning. Retain per-task configurations and metrics. Field: `links:family:discovery-model-esm3` Claim: model-evaluation-identity-436d088fde334db49648 Source artifact SHA-256: `59c7bbb888e8e91f33c1e2cabfde062c32381d6ca727d23b6655c977aabf97a2` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

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Sources and history

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Release 2026-09-29-06401fd5b220 · Record review: source checked

1 source records and release history

pfmbench primary benchmark evidence · Original source · 2506.14796v1

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Technical metadata and extraction receipts

Stable ID: pfmbench-method-esm3

areas: proteins-complexes
source locator: Table 3, row(ESM3 [ 18 ])
missing metadata: checkpoint revision: unreported; parameters: unextracted

Related records

family: ESM3
subject: ESM3: family ESM3
model: ESM3 on PFMBench ANTI-RES: Antibiotic resistance
model: ESM3 on PFMBench BINDING-DB: BindingDB
model: ESM3 on PFMBench CLONING-CLF: Cloning CLF
model: ESM3 on PFMBench DEEPLOC2: DeepLoc2 Multi
model: ESM3 on PFMBench DEEPSOL: DeepSol
model: ESM3 on PFMBench EC: Enzyme Commission
model: ESM3 on PFMBench MAT-PROD: Material production
model: ESM3 on PFMBench METAL-ION: Metal ion binding
model: ESM3 on PFMBench PDB-BIND: PDBbind
model: ESM3 on PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction
model: ESM3 on PFMBench SEC-STRUCT: Secondary structure
model: ESM3 on PFMBench STABILITY: TAPE_Stability

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