Model type
Multitrack generative protein transformer
ESM3 generates and completes protein sequence, structure and functional annotations using a shared multimodal representation.
Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.
Multitrack generative protein transformer
Complete or partial protein sequence, structure and function-keyword tracks.
Completed sequence, structure and functional tracks.
Official project documentation and implementation: https://github.com/evolutionaryscale/esm
limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
20 evaluations · 20 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-100-DIVERSITY-MAX-CLUST: length 100, Diversity Max Clust. Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 0.9 max-clust score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-100-DIVERSITY-MAX-CLUST: length 100, Diversity Max Clust. Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 100, Diversity Max Clust. ↑) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-100-DIVERSITY-PAIRWISE-TM: length 100, Diversity pairwise TM Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 0.45 ± 0.15 pairwise-tm score · lower Uncertainty: type: standard_deviation; value: 0.15 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-100-DIVERSITY-PAIRWISE-TM: length 100, Diversity pairwise TM Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 100, Diversity pairwise TM ↓) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-100-NOVELTY-MAX-TM: length 100, Novelty Max TM Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 0.68 ± 0.07 max-tm score · lower Uncertainty: type: standard_deviation; value: 0.07 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-100-NOVELTY-MAX-TM: length 100, Novelty Max TM Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 100, Novelty Max TM ↓) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-100-QUALITY-PLDDT: length 100, Quality pLDDT Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 54.26 ± 15.35 plddt score · higher Uncertainty: type: standard_deviation; value: 15.35 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-100-QUALITY-PLDDT: length 100, Quality pLDDT Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 100, Quality pLDDT ↑) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-100-QUALITY-PPL: length 100, Quality ppl Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 14.79 ± 2.90 ppl score · lower Uncertainty: type: standard_deviation; value: 2.90 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-100-QUALITY-PPL: length 100, Quality ppl Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 100, Quality ppl ↓) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-200-DIVERSITY-MAX-CLUST: length 200, Diversity Max Clust. Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 1 max-clust score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-200-DIVERSITY-MAX-CLUST: length 200, Diversity Max Clust. Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 200, Diversity Max Clust. ↑) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-200-DIVERSITY-PAIRWISE-TM: length 200, Diversity pairwise TM Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 0.35 ± 0.07 pairwise-tm score · lower Uncertainty: type: standard_deviation; value: 0.07 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-200-DIVERSITY-PAIRWISE-TM: length 200, Diversity pairwise TM Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 200, Diversity pairwise TM ↓) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-200-NOVELTY-MAX-TM: length 200, Novelty Max TM Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 0.80 ± 0.01 max-tm score · lower Uncertainty: type: standard_deviation; value: 0.01 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-200-NOVELTY-MAX-TM: length 200, Novelty Max TM Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 200, Novelty Max TM ↓) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-200-QUALITY-PLDDT: length 200, Quality pLDDT Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 58.45 ± 9.40 plddt score · higher Uncertainty: type: standard_deviation; value: 9.40 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-200-QUALITY-PLDDT: length 200, Quality pLDDT Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 200, Quality pLDDT↑) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-200-QUALITY-PPL: length 200, Quality ppl Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 12.96 ± 2.38 ppl score · lower Uncertainty: type: standard_deviation; value: 2.38 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-200-QUALITY-PPL: length 200, Quality ppl Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 200, Quality ppl ↓) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-300-DIVERSITY-MAX-CLUST: length 300, Diversity Max Clust. Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 1 max-clust score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-300-DIVERSITY-MAX-CLUST: length 300, Diversity Max Clust. Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 300, Diversity Max Clust. ↑) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-300-DIVERSITY-PAIRWISE-TM: length 300, Diversity pairwise TM Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 0.32 ± 0.03 pairwise-tm score · lower Uncertainty: type: standard_deviation; value: 0.03 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-300-DIVERSITY-PAIRWISE-TM: length 300, Diversity pairwise TM Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 300, Diversity pairwise TM ↓) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-300-NOVELTY-MAX-TM: length 300, Novelty Max TM Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 0.75 ± 0.02 max-tm score · lower Uncertainty: type: standard_deviation; value: 0.02 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-300-NOVELTY-MAX-TM: length 300, Novelty Max TM Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 300, Novelty Max TM ↓) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-300-QUALITY-PLDDT: length 300, Quality pLDDT Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 48.08 ± 13.34 plddt score · higher Uncertainty: type: standard_deviation; value: 13.34 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-300-QUALITY-PLDDT: length 300, Quality pLDDT Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 300, Quality pLDDT ↑) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-300-QUALITY-PPL: length 300, Quality ppl Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 14.59 ± 2.97 ppl score · lower Uncertainty: type: standard_deviation; value: 2.97 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-300-QUALITY-PPL: length 300, Quality ppl Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 300, Quality ppl ↓) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-500-DIVERSITY-MAX-CLUST: length 500, Diversity Max Clust. Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 1 max-clust score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-500-DIVERSITY-MAX-CLUST: length 500, Diversity Max Clust. Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 500, Diversity Max Clust. ↑) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-500-DIVERSITY-PAIRWISE-TM: length 500, Diversity pairwise TM Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 0.30 ± 0.05 pairwise-tm score · lower Uncertainty: type: standard_deviation; value: 0.05 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-500-DIVERSITY-PAIRWISE-TM: length 500, Diversity pairwise TM Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 500, Diversity pairwise TM ↓) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-500-NOVELTY-MAX-TM: length 500, Novelty Max TM Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 0.54 ± 0.03 max-tm score · lower Uncertainty: type: standard_deviation; value: 0.03 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-500-NOVELTY-MAX-TM: length 500, Novelty Max TM Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 500, Novelty Max TM ↓) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-500-QUALITY-PLDDT: length 500, Quality pLDDT Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 52.17 ± 10.52 plddt score · higher Uncertainty: type: standard_deviation; value: 10.52 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-500-QUALITY-PLDDT: length 500, Quality pLDDT Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 500, Quality pLDDT↑) |
| Configuration: ESM3 (1.4B) | Task: ProteinBench SEQ-LENGTH-500-QUALITY-PPL: length 500, Quality ppl Dataset subset: Generated sequences at fixed lengths (ProteinBench split) | 11.10 ± 2.26 ppl score · lower Uncertainty: type: standard_deviation; value: 2.26 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM3 (1.4B) on ProteinBench SEQ-LENGTH-500-QUALITY-PPL: length 500, Quality ppl Unconditional sequence generation at a fixed length. Values are the mean and standard deviation over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 4, row(ESM3 (1.4B)), column(length 500, Quality ppl ↓) |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Related profile: ESM3. This page retains the exact record and its evaluation context.
Protein model evaluated by the ProteinBench authors under their harness.
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.
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.
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-esm3Explanatory 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.
| Property | Description and evidence |
|---|---|
| Model type | Multitrack generative protein transformerSources (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 sourcesSources (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 sourcesSources (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/esmSources (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 | MITSourcesevolutionaryscale/esm: LICENSE.md · LICENSE.md: licence text |
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
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
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: family discovery-model-esm3 Individual claims | proteinbench primary benchmark evidence Tables 4; task methods and corresponding named row Version: 2409.06744v1 | source checked automated source review · 2026-09-23 Audit detailsSource review establishes this relationship only. Exact evaluated configurations and original numerical review status remain unchanged. Paper evaluates this named model under its ProteinBench harness. Association is to the family, not an assertion of checkpoint equivalence or cross-task comparability. Field: Claim: model-evaluation-identity-46356b20adbab40c94a9 Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
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Release 2026-09-29-06401fd5b220 · Record review: source checked
Stable ID: proteinbench-method-esm3-1-4b