Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Task
DNA-binding residue prediction
DNA-binding residue prediction uses published protein-sequence training and independent test collections.
Sources
MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captionsAt a glance
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 |
|---|---|
| Datasets | DNA-573_Train, DNA-129_Test and DNA-181_Test from prior binding-site benchmarks.SourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions |
| Splits | Published training/test collections are maintained and similarity filtering is applied.SourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions |
| Metrics | AUC, average precision and MCC are central comparison metrics; specificity and precision are also reported.SourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions |
| Baselines | ESM2, ProtTrans, ProteinBERT and ESM3 embedding variants evaluated on the same named residue-label test collections.SourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions |
| Leakage controls | The source describes a 30% sequence-identity clustering cutoff between training and test sequences.SourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions |
| Uncertainty | The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. · Not reported in inspected sourcesSourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions |
| Entity type | Paper-specific computational evaluation protocol.SourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions |
| Organisms | The DNA-binding test uses the GraphBind/GraphSite DNA protein collections. The benchmark-data section and Table 1 describe proteins and residue labels without a species inventory; the separate RNA-binding collections do not define this task’s taxa. · Not reported in inspected sourcesSourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Benchmark datasets and Table 1 |
| Assays | Curated DNA-binding residue labels.SourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions |
| Allowed inputs | Protein representations for residue-level prediction.SourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions |
| Adaptation | Supervised binding-site prediction on the published training set.SourcesMegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions |
How it works
How it worksComputational evaluation flow
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Sources
MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captionsEvaluation methodology
DNA-573_Train, DNA-129_Test and DNA-181_Test from prior binding-site benchmarks. Published training/test collections are maintained and similarity filtering is applied. AUC, average precision and MCC are central comparison metrics; specificity and precision are also reported. ESM2, ProtTrans, ProteinBERT and ESM3 embedding variants evaluated on the same named residue-label test collections. The source describes a 30% sequence-identity clustering cutoff between training and test sequences. The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim.
Sources
MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captionsRecorded evaluations
Each evaluation records what was tested and under which conditions.
Tested entities 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. |
Papers and result coverage
Last literature check: 2026-09-17. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
| Paper or primary resource | Version | Reference |
|---|---|---|
| MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model | journal full text in PMC | Read source DOI: 10.1093/bib/bbaf524 |
What is still missing
- Complete raw table acquired. Assigned benchmark is DNA-binding; RNA cohorts need distinct protocols. PCC-to-MegSite agreement and associatedPvalues are not predictive performance. Structured extraction pending.
Search and extraction details
source found structured extraction pending
Searches
- MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model primary paper benchmark results
Evidence locations
- Table3 DNA129/DNA181/RNA117/RNA285 comparison
Strengths and limitations
Limitations and conditions
- The paper separately evaluates RNA-binding sites; RNA structural split details must not be imported into this DNA-binding result.
Sources
MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions
Profile review details
Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged.
Stable record: reported-task-9917a0e69f33e7Evidence 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.
17 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Input: Protein representations for residue-level prediction.","Evaluation: Supervised binding-site prediction on the published training set.","Readout: AUC, average precision and MCC are central comparison metrics; specificity and precision are also reported."] Individual claims | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets DNA-573_Train, DNA-129_Test and DNA-181_Test from prior binding-site benchmarks. Individual claims | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits Published training/test collections are maintained and similarity filtering is applied. Individual claims | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Supervised binding-site prediction on the published training set. Individual claims | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics AUC, average precision and MCC are central comparison metrics; specificity and precision are also reported. Individual claims | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines ESM2, ProtTrans, ProteinBERT and ESM3 embedding variants evaluated on the same named residue-label test collections. Individual claims | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls The source describes a 30% sequence-identity clustering cutoff between training and test sequences. Individual claims | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Uncertainty The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. Individual claims | MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions Version: journal full text in PMC | unreported automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. 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
- MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model · Original source · journal full text in PMC
Technical metadata and extraction receipts
Stable ID: reported-task-9917a0e69f33e7
- areas
- proteins-complexes
- tasks
- DNA-binding residue prediction
- entity level
- task
- version
- Not reported
- task
- DNA-binding residue prediction
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- benchmark research
- review date: 2026-09-17; status: source_found_structured_extraction_pending; primary sources: evidence-expansion-p2-megsite-2025-10d131223318; inspected locators: Table3 DNA129/DNA181/RNA117/RNA285 comparison; searched queries: MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model primary paper benchmark results; gaps: Complete raw table acquired. Assigned benchmark is DNA-binding; RNA cohorts need distinct protocols. PCC-to-MegSite agreement and associatedPvalues are not predictive performance. Structured extraction pending.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
- historical missing metadata
- protocol version: 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
- benchmark
- entity classification
- review date: 2026-09-17; rationale: This source-scoped record identifies the biological prediction task and holds its paper context. Preserve the existing task identity; exact split, model adaptation and scoring remain in linked evaluations or separate protocol records.; source ids: megsite-2025; source locator: Methods: Benchmark datasets; Results; cached text lines 9–10, 63; matching task comparison table/ablation captions; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.; Some legacy profile Entity type facts use the generic phrase computational evaluation protocol. That boilerplate is not sufficient to establish a single fixed protocol identity or to merge this task with another protocol record.
Related records
- dataset: DNA-129_Test
- benchmark: MegSite + ESM3: DNA-binding residue prediction