Model type
Study-specific predictive method; this record is the paper-specific evaluated configuration.
Pipeline
MegSite + ESM3
MegSite predicts protein residues that bind DNA or RNA using multimodal ESM3 information.
Sources
MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Bidirectional cross-attention fusion/The architecture of MegSite (paragraph 1); Bidirectional cross-attention fusion/Implementation details (paragraph 2)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
MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Results/Performance of different network architectures (paragraph 7); Materials and methods/Multimodal protein language model (paragraph 2)At a glance
Biological inputs
Protein sequence, structure and function representations
Sources
MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Results/Comparison with alternative protein language model embeddings (paragraph 3); Protein graph representation/Node feature (paragraph 1)Outputs
Per-residue DNA- or RNA-binding predictions
Sources
MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Results/Comparison with state-of-the-art methods (paragraph 3); Protein graph representation (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 · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| MegSite + ESM3: DNA-binding residue prediction ESM3 multimodal embedding ablation in MegSite Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.948 AUC Unit: fraction · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Table 2, DNA-129_Test / ESM3 row, AUC column Source checking is not independent reproduction. |
How it works
How the evaluated method works
Sequence, structural and functional representations from ESM3 inform a task-specific nucleic-acid-binding-site predictor.
Sources
MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Results/Performance of different network architectures (paragraph 7); Materials and methods/Multimodal protein language model (paragraph 2)What was evaluated
The linked evaluation record identifies MegSite + ESM3: DNA-binding residue prediction. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-b2-megsite-2025Strengths and limitations
Strengths and considerations
- Includes independent tests and analyses of proteins with low structural similarity.
Sources
MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Results/Performance of different network architectures (paragraph 6); Abstract (paragraph 1)
Limitations and conditions
- These are downstream binding-site predictions with multimodal inputs, not raw ESM3 outputs or evidence that predicted binding is experimentally realised.
Sources
MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Bidirectional cross-attention fusion/The architecture of MegSite (paragraph 1); Results/Comparison with alternative protein language model embeddings (paragraph 3)
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-86393c76dd8fa9Specifications
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 | Study-specific predictive method; this record is the paper-specific evaluated configuration.SourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Results/Performance of different network architectures (paragraph 7); Materials and methods/Multimodal protein language model (paragraph 2) |
| Architecture / procedure | Sequence, structural and functional representations from ESM3 inform a task-specific nucleic-acid-binding-site predictor.SourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Results/Performance of different network architectures (paragraph 7); Materials and methods/Multimodal protein language model (paragraph 2) |
| Biological inputs | Protein sequence, structure and function representationsSourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Results/Comparison with alternative protein language model embeddings (paragraph 3); Protein graph representation/Node feature (paragraph 1) |
| Outputs | Per-residue DNA- or RNA-binding predictionsSourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Results/Comparison with state-of-the-art methods (paragraph 3); Protein graph representation (paragraph 1) |
| Parameters | The feature extractor is ESM3-Small: 1.4 billion parameters and 48 transformer blocks. The equivariant graph predictor is an additional fitted component.SourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Materials and methods/Multimodal protein language model (paragraph 2); Protein graph representation/Node feature (paragraph 1) |
| Known versions / configuration | MegSite + ESM3 is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sourcesSourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. |
| Training data / fitting | DNA-573_Train and RNA-495_Train with independent DNA/RNA test sets; the paper filters training/test sequence similarity at 30%.SourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Materials and methods/Benchmark datasets (paragraph 1); Results/Comparison with state-of-the-art methods (paragraph 1) |
| 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)MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model; pengsl-lab/MegSite README.md · Materials and methods/Benchmark datasets; Materials and methods/Multimodal protein language model; Bidirectional cross-attention fusion/Implementation details; Bidirectional cross-attention fusion/The architecture of MegSite; Results/Performance of different network architectures; Results/Comparison with state-of-the-art methods; inspected for explicit maximum input length (dataset lengths and family-wide limits are not substituted); README.md at pinned repository revision |
| Access | Official study implementation and usage documentation: https://github.com/pengsl-lab/MegSite/blob/4d1f5441f15bd20eb3e7c9e5be2d4ca5a857f46b/README.md. This pinned documentation revision is not automatically the evaluated weight revision.Sourcespengsl-lab/MegSite README.md · README.md; installation, model download and usage instructions |
| Code licence | No explicit code licence was established from the paper’s availability statement and inspected repository-root documentation. · Not reported in inspected sourcesSourcespengsl-lab/MegSite README.md · README.md and repository-root licence-file search |
| 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 sourcesSourcespengsl-lab/MegSite 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.
20 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 | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Results/Performance of different network architectures (paragraph 7); Materials and methods/Multimodal protein language model (paragraph 2) Version: journal full text in PMC | 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 ["Protein sequence, structure and function representations","MegSite + ESM3","Per-residue DNA- or RNA-binding predictions"] Individual claims | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Results/Performance of different network architectures (paragraph 7); Materials and methods/Multimodal protein language model (paragraph 2) Version: journal full text in PMC | 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 | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Results/Performance of different network architectures (paragraph 7); Materials and methods/Multimodal protein language model (paragraph 2) Version: journal full text in PMC | 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 Study-specific predictive method; this record is the paper-specific evaluated configuration. Individual claims | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Results/Performance of different network architectures (paragraph 7); Materials and methods/Multimodal protein language model (paragraph 2) Version: journal full text in PMC | 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 Sequence, structural and functional representations from ESM3 inform a task-specific nucleic-acid-binding-site predictor. Individual claims | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Results/Performance of different network architectures (paragraph 7); Materials and methods/Multimodal protein language model (paragraph 2) Version: journal full text in PMC | 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 | pengsl-lab/MegSite README.md README.md; checkpoint/access documentation and licence scope Version: 4d1f5441f15bd20eb3e7c9e5be2d4ca5a857f46b | 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 Protein sequence, structure and function representations Individual claims | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Results/Comparison with alternative protein language model embeddings (paragraph 3); Protein graph representation/Node feature (paragraph 1) Version: journal full text in PMC | 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 Per-residue DNA- or RNA-binding predictions Individual claims | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Results/Comparison with state-of-the-art methods (paragraph 3); Protein graph representation (paragraph 1) Version: journal full text in PMC | 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 The feature extractor is ESM3-Small: 1.4 billion parameters and 48 transformer blocks. The equivariant graph predictor is an additional fitted component. Individual claims | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Materials and methods/Multimodal protein language model (paragraph 2); Protein graph representation/Node feature (paragraph 1) Version: journal full text in PMC | 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 MegSite + ESM3 is the comparison-table label; that label does not specify an immutable weight revision. Individual claims | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. Version: journal full text in PMC | 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
2 source records and release history
- MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Original source · journal full text in PMC
- pengsl-lab/MegSite README.md · Original source · 4d1f5441f15bd20eb3e7c9e5be2d4ca5a857f46b
Technical metadata and extraction receipts
Stable ID: reported-model-86393c76dd8fa9
- areas
- proteins-complexes
- entity level
- method
- version
- not stated in table
- reported name
- MegSite + ESM3
- historical missing metadata
- 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 record identifies a composed analysis workflow with separately identifiable upstream models, representations or tools and a downstream prediction/scoring procedure. Results belong to that complete composition rather than to an upstream model alone.; source ids: megsite-2025; source locator: Results/Performance of different network architectures (paragraph 7); Materials and methods/Multimodal protein language model (paragraph 2) | Bidirectional cross-attention fusion/The architecture of MegSite (paragraph 1); Bidirectional cross-attention fusion/Implementation details (paragraph 2); ambiguities: This is the paper-specific pipeline identity; unspecified component checkpoints or implementation versions are not inferred from its name.