Model type
Protein sequence transformer; this record is the paper-specific evaluated configuration.
Configuration
ESM2
This FUJISAN-study baseline compares proteins by cosine similarity between mean ESM-2 embeddings.
Sources
Enhanced prediction of protein functional identity through the integration of sequence and structural features · Materials and methods/Prediction with ESM-2 (paragraph 2); Results and discussion/Limitations and perspectives (paragraph 1)How it worksEvaluated procedure (conceptual)
Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings.
Sources
Enhanced prediction of protein functional identity through the integration of sequence and structural features · Materials and methods/Prediction with ESM-2 (paragraph 2); Materials and methods/Prediction with DeepFRI (paragraph 1)At a glance
Biological inputs
Pairs of protein amino-acid sequences
Sources
Enhanced prediction of protein functional identity through the integration of sequence and structural features · Materials and methods/Prediction with ESM-2 (paragraph 1); Introduction (paragraph 4)Outputs
Pairwise cosine similarity used as a same-function score
Sources
Enhanced prediction of protein functional identity through the integration of sequence and structural features · Materials and methods/Prediction with ESM-2 (paragraph 2); Materials and methods/Prediction with DeepFRI (paragraph 1)limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
Release 2026-09-17-d277315f7d76 · 1 evaluation · 8 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| ESM2: Enzyme functional identity prediction Configuration: ESM2Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction)Dataset: FUJISAN test sub-dataset LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.7991 AUROC Unit: unitless · Direction: higher | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features; Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, ESM2 row, AUROC column Source checking is not independent reproduction. |
| 79.33% REC (%) Unit: percent · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row ESM2, column REC (%); XML row5 column4 Source checking is not independent reproduction. |
| 0.8147 AUPR Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row ESM2, column AUPR; XML row5 column9 Source checking is not independent reproduction. |
| 0.4321 MCC Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row ESM2, column MCC; XML row5 column7 Source checking is not independent reproduction. |
| 68.39% PRE (%) Unit: percent · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row ESM2, column PRE (%); XML row5 column3 Source checking is not independent reproduction. |
| 0.7345 F1 Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row ESM2, column F1; XML row5 column6 Source checking is not independent reproduction. |
| 71.33% ACC (%) Unit: percent · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row ESM2, column ACC (%); XML row5 column2 Source checking is not independent reproduction. |
| 36.67% FPR (%) Unit: percent · Direction: lower | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row ESM2, column FPR (%); XML row5 column5 Source checking is not independent reproduction. |
How it works
How the evaluated method works
esm2_t33_650M_UR50D emits 1,280-dimensional residue vectors. Mean pooling gives a protein vector; cosine similarity estimates whether two proteins share an enzymatic function.
Sources
Enhanced prediction of protein functional identity through the integration of sequence and structural features · Materials and methods/Prediction with ESM-2 (paragraph 2); Materials and methods/Prediction with DeepFRI (paragraph 1)Underlying method and version boundaries
ESM-2 is a transformer protein language-model family. The official repository exposes residue embeddings, sequence-level pooling and models at several sizes; the study configuration determines which of these is evaluated.
Sources
facebookresearch/esm README.md · README.md; introduction, model description, pretrained-model and usage sections at pinned revisionWhat was evaluated
The linked evaluation record identifies ESM2: Enzyme functional identity prediction. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
Enhanced prediction of protein functional identity through the integration of sequence and structural features · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-020Strengths and limitations
Strengths and considerations
- A simple sequence-only representation baseline with an explicit pooling and scoring rule.
Sources
Enhanced prediction of protein functional identity through the integration of sequence and structural features · Materials and methods/Prediction with ESM-2 (paragraph 1); Materials and methods/Feature engineering/Pocket similarity features (paragraph 1)
Limitations and conditions
- Cosine similarity is a proxy for functional similarity, not a calibrated catalytic-function probability.
Sources
Enhanced prediction of protein functional identity through the integration of sequence and structural features · Materials and methods/Prediction with ESM-2 (paragraph 2); Conclusions (paragraph 1)
Profile review details
Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction.
Stable record: reported-model-ccd1160ad4ec27Specifications
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.
| Property | Description and evidence |
|---|---|
| Model type | Protein sequence transformer; this record is the paper-specific evaluated configuration.Sourcesfacebookresearch/esm README.md · README.md model description |
| Architecture / procedure | esm2_t33_650M_UR50D emits 1,280-dimensional residue vectors. Mean pooling gives a protein vector; cosine similarity estimates whether two proteins share an enzymatic function.SourcesEnhanced prediction of protein functional identity through the integration of sequence and structural features · Materials and methods/Prediction with ESM-2 (paragraph 2); Materials and methods/Prediction with DeepFRI (paragraph 1) |
| Biological inputs | Pairs of protein amino-acid sequencesSourcesEnhanced prediction of protein functional identity through the integration of sequence and structural features · Materials and methods/Prediction with ESM-2 (paragraph 1); Introduction (paragraph 4) |
| Outputs | Pairwise cosine similarity used as a same-function scoreSourcesEnhanced prediction of protein functional identity through the integration of sequence and structural features · Materials and methods/Prediction with ESM-2 (paragraph 2); Materials and methods/Prediction with DeepFRI (paragraph 1) |
| Parameters | 650 million backbone parameters; no FUJISAN LightGBM features are part of this comparator.SourcesEnhanced prediction of protein functional identity through the integration of sequence and structural features · Results and discussion/Analysis of feature importance (paragraph 1); Materials and methods/Model training and hyperparameter optimization (paragraph 1) |
| Known versions / configuration | esm2_t33_650M_UR50D · Not reported in inspected sourcesSourcesEnhanced prediction of protein functional identity through the integration of sequence and structural features · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. |
| Training data / fitting | The comparator uses pretrained ESM-2 sequence embeddings and cosine similarity; it does not fit FUJISAN’s LightGBM head or a task-specific interaction classifier.SourcesEnhanced prediction of protein functional identity through the integration of sequence and structural features · ESM2 embedding comparator and cosine-similarity procedure |
| Context limits | A maximum input/context length for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)Enhanced prediction of protein functional identity through the integration of sequence and structural features; facebookresearch/esm README.md · Materials and methods/Dataset construction; Materials and methods/Feature engineering/Full-length sequence similarity features; Materials and methods/Feature engineering/Domain structural similarity features; Materials and methods/Feature engineering/Pocket similarity features; Materials and methods/Model training and hyperparameter optimization; Materials and methods/Performance assessment; Materials and methods/Prediction with DeepFRI; Materials and methods/Prediction with ESM-2; inspected for explicit maximum input length (dataset lengths and family-wide limits are not substituted); README.md at pinned repository revision |
| Access | Official upstream implementation and usage documentation: https://github.com/facebookresearch/esm/blob/2b369911bb5b4b0dda914521b9475cad1656b2ac/README.md. This pinned documentation revision is not automatically the evaluated weight revision.Sourcesfacebookresearch/esm README.md · README.md; installation, model download and usage instructions |
| Code licence | MIT (upstream repository code at the cited revision; this does not establish every dependency or historical checkpoint licence).Sourcesfacebookresearch/esm LICENSE · LICENSE; complete licence text |
| Weights licence | The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. · Not reported in inspected sourcesSourcesfacebookresearch/esm README.md · README.md; checkpoint/access documentation and licence scope |
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.
21 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings. Individual claims | Enhanced prediction of protein functional identity through the integration of sequence and structural features Materials and methods/Prediction with ESM-2 (paragraph 2); Materials and methods/Prediction with DeepFRI (paragraph 1) Version: PMC11609699.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Pairs of protein amino-acid sequences","ESM2","Pairwise cosine similarity used as a same-function score"] Individual claims | Enhanced prediction of protein functional identity through the integration of sequence and structural features Materials and methods/Prediction with ESM-2 (paragraph 2); Materials and methods/Prediction with DeepFRI (paragraph 1) Version: PMC11609699.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Evaluated procedure (conceptual) Individual claims | Enhanced prediction of protein functional identity through the integration of sequence and structural features Materials and methods/Prediction with ESM-2 (paragraph 2); Materials and methods/Prediction with DeepFRI (paragraph 1) Version: PMC11609699.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Model type Protein sequence transformer; this record is the paper-specific evaluated configuration. Individual claims | facebookresearch/esm README.md README.md model description Version: 2b369911bb5b4b0dda914521b9475cad1656b2ac | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Architecture / procedure esm2_t33_650M_UR50D emits 1,280-dimensional residue vectors. Mean pooling gives a protein vector; cosine similarity estimates whether two proteins share an enzymatic function. Individual claims | Enhanced prediction of protein functional identity through the integration of sequence and structural features Materials and methods/Prediction with ESM-2 (paragraph 2); Materials and methods/Prediction with DeepFRI (paragraph 1) Version: PMC11609699.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Weights licence The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. Individual claims | facebookresearch/esm README.md README.md; checkpoint/access documentation and licence scope Version: 2b369911bb5b4b0dda914521b9475cad1656b2ac | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Biological inputs Pairs of protein amino-acid sequences Individual claims | Enhanced prediction of protein functional identity through the integration of sequence and structural features Materials and methods/Prediction with ESM-2 (paragraph 1); Introduction (paragraph 4) Version: PMC11609699.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Outputs Pairwise cosine similarity used as a same-function score Individual claims | Enhanced prediction of protein functional identity through the integration of sequence and structural features Materials and methods/Prediction with ESM-2 (paragraph 2); Materials and methods/Prediction with DeepFRI (paragraph 1) Version: PMC11609699.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters 650 million backbone parameters; no FUJISAN LightGBM features are part of this comparator. Individual claims | Enhanced prediction of protein functional identity through the integration of sequence and structural features Results and discussion/Analysis of feature importance (paragraph 1); Materials and methods/Model training and hyperparameter optimization (paragraph 1) Version: PMC11609699.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Known versions / configuration esm2_t33_650M_UR50D Individual claims | Enhanced prediction of protein functional identity through the integration of sequence and structural features Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. Version: PMC11609699.1 | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
3 source records and release history
- Enhanced prediction of protein functional identity through the integration of sequence and structural features · Original source · PMC11609699.1
- facebookresearch/esm README.md · Original source · 2b369911bb5b4b0dda914521b9475cad1656b2ac
- facebookresearch/esm LICENSE · Original source · 2b369911bb5b4b0dda914521b9475cad1656b2ac
Technical metadata and extraction receipts
Stable ID: reported-model-ccd1160ad4ec27
- areas
- proteins-complexes
- entity level
- method
- version
- Not reported
- reported name
- ESM2
- historical missing metadata
- version: not_reported_in_legacy_extract; checkpoint revision: not_reported_in_legacy_extract; training data: not_reported_in_legacy_extract; licence: not_reported_in_legacy_extract
- metadata review scope
- historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
- legacy kinds
- model
- entity classification
- review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: fujisan-2024; evidence-reported-base-esm-readme-md; source locator: Materials and methods/Prediction with ESM-2 (paragraph 2); Materials and methods/Prediction with DeepFRI (paragraph 1) | README.md model description | Materials and methods/Prediction with ESM-2 (paragraph 2); Results and discussion/Limitations and perspectives (paragraph 1); ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.