Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Task
RNA-small-molecule binding-site prediction
RNA small-molecule binding-site prediction uses independent RNA–ligand test collections with explicit redundancy filtering.
Sources
RNA language model and graph attention network for RNA and small molecule binding sites prediction · Methods §§2.1, 2.7; cached text lines 13–15, 57–58At 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 | Combined RNAglib/RNAsite training data; T18, T3 and newly curated T10 tests.SourcesRNA language model and graph attention network for RNA and small molecule binding sites prediction · Methods §§2.1, 2.7; cached text lines 13–15, 57–58 |
| Splits | The named test collections are held separate; T10 uses later PDB entries.SourcesRNA language model and graph attention network for RNA and small molecule binding sites prediction · Methods §§2.1, 2.7; cached text lines 13–15, 57–58 |
| Metrics | Precision, recall, MCC and ROC-AUC.SourcesRNA language model and graph attention network for RNA and small molecule binding sites prediction · Methods §§2.1, 2.7; cached text lines 13–15, 57–58 |
| Baselines | Training data align with MultiModRLBP for comparison.SourcesRNA language model and graph attention network for RNA and small molecule binding sites prediction · Methods §§2.1, 2.7; cached text lines 13–15, 57–58 |
| Leakage controls | T3 removes high-similarity RNAs relative to training; T10 is clustered and filtered against training RNA.SourcesRNA language model and graph attention network for RNA and small molecule binding sites prediction · Methods §§2.1, 2.7; cached text lines 13–15, 57–58 |
| Uncertainty | The paper reports t-tests comparing metrics; the exact replication unit should be confirmed before interpreting them as independent-sample uncertainty.SourcesRNA language model and graph attention network for RNA and small molecule binding sites prediction · Methods §§2.1, 2.7; cached text lines 13–15, 57–58 |
| Entity type | Paper-specific computational evaluation protocol.SourcesRNA language model and graph attention network for RNA and small molecule binding sites prediction · Methods §§2.1, 2.7; cached text lines 13–15, 57–58 |
| Organisms | RNAglib/RNAsite-derived RNA chains and PDB-derived test sets define this benchmark. Section 2.1 reports chain and ligand membership criteria but not a taxonomic inventory; synthetic aptamer examples cannot be assigned an organism from the surrounding disease discussion. · Not reported in inspected sourcesSourcesRNA language model and graph attention network for RNA and small molecule binding sites prediction · §2.1 Benchmark datasets; RNA–ligand test examples |
| Assays | RNA–small-molecule binding-site annotations.SourcesRNA language model and graph attention network for RNA and small molecule binding sites prediction · Methods §§2.1, 2.7; cached text lines 13–15, 57–58 |
| Allowed inputs | RNA representations for site prediction.SourcesRNA language model and graph attention network for RNA and small molecule binding sites prediction · Methods §§2.1, 2.7; cached text lines 13–15, 57–58 |
| Adaptation | Supervised fitting on the combined training data; later PDB entries supply one held-out test.SourcesRNA language model and graph attention network for RNA and small molecule binding sites prediction · Methods §§2.1, 2.7; cached text lines 13–15, 57–58 |
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
RNA language model and graph attention network for RNA and small molecule binding sites prediction · Methods §§2.1, 2.7; cached text lines 13–15, 57–58Evaluation methodology
Combined RNAglib/RNAsite training data; T18, T3 and newly curated T10 tests. The named test collections are held separate; T10 uses later PDB entries. Precision, recall, MCC and ROC-AUC. Training data align with MultiModRLBP for comparison. T3 removes high-similarity RNAs relative to training; T10 is clustered and filtered against training RNA. The paper reports t-tests comparing metrics; the exact replication unit should be confirmed before interpreting them as independent-sample uncertainty.
Sources
RNA language model and graph attention network for RNA and small molecule binding sites prediction · Methods §§2.1, 2.7; cached text lines 13–15, 57–58Recorded 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 |
|---|---|---|
| RLsite: RNA-small-molecule binding-site prediction RNA language-model plus graph-attention classifier Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.828 AUC Unit: fraction · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedRNA language model and graph attention network for RNA and small molecule binding sites prediction · Table 1, RLsite row, T18 AUC column Source checking is not independent reproduction. |
Papers and result coverage
Last literature check: 2026-09-17. Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.
| Paper or primary resource | Version | Reference |
|---|---|---|
| RNA language model and graph attention network for RNA and small molecule binding sites prediction | journal full text in PMC | Read source DOI: 10.1093/bioinformatics/btaf447 |
What is still missing
- Most baseline values are copied from original publications; RNABind is a web-server run.
- T18/T3/T10 are separate protocols and cannot be pooled as one model score.
- Unavailable RNet AUC is a dash, not zero.
Search and extraction details
primary comparison table screened
Searches
- "PMC12417085"
Evidence locations
- Tables 1–3 footnotes
- Section 2.1 Benchmark datasets
Strengths and limitations
Limitations and conditions
- Small RNA test sets limit the number of independent examples. Chain/sequence exclusions do not by themselves establish ligand-disjoint evaluation.
Sources
RNA language model and graph attention network for RNA and small molecule binding sites prediction · Methods §§2.1, 2.7; cached text lines 13–15, 57–58
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-b00a636d1ed8d9Evidence 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 | RNA language model and graph attention network for RNA and small molecule binding sites prediction Methods §§2.1, 2.7; cached text lines 13–15, 57–58 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: RNA representations for site prediction.","Evaluation: Supervised fitting on the combined training data; later PDB entries supply one held-out test.","Readout: Precision, recall, MCC and ROC-AUC."] Individual claims | RNA language model and graph attention network for RNA and small molecule binding sites prediction Methods §§2.1, 2.7; cached text lines 13–15, 57–58 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 | RNA language model and graph attention network for RNA and small molecule binding sites prediction Methods §§2.1, 2.7; cached text lines 13–15, 57–58 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 Combined RNAglib/RNAsite training data; T18, T3 and newly curated T10 tests. Individual claims | RNA language model and graph attention network for RNA and small molecule binding sites prediction Methods §§2.1, 2.7; cached text lines 13–15, 57–58 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 The named test collections are held separate; T10 uses later PDB entries. Individual claims | RNA language model and graph attention network for RNA and small molecule binding sites prediction Methods §§2.1, 2.7; cached text lines 13–15, 57–58 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 fitting on the combined training data; later PDB entries supply one held-out test. Individual claims | RNA language model and graph attention network for RNA and small molecule binding sites prediction Methods §§2.1, 2.7; cached text lines 13–15, 57–58 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 Precision, recall, MCC and ROC-AUC. Individual claims | RNA language model and graph attention network for RNA and small molecule binding sites prediction Methods §§2.1, 2.7; cached text lines 13–15, 57–58 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 Training data align with MultiModRLBP for comparison. Individual claims | RNA language model and graph attention network for RNA and small molecule binding sites prediction Methods §§2.1, 2.7; cached text lines 13–15, 57–58 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 T3 removes high-similarity RNAs relative to training; T10 is clustered and filtered against training RNA. Individual claims | RNA language model and graph attention network for RNA and small molecule binding sites prediction Methods §§2.1, 2.7; cached text lines 13–15, 57–58 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 paper reports t-tests comparing metrics; the exact replication unit should be confirmed before interpreting them as independent-sample uncertainty. Individual claims | RNA language model and graph attention network for RNA and small molecule binding sites prediction Methods §§2.1, 2.7; cached text lines 13–15, 57–58 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 |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
2 source records and release history
- RNA language model and graph attention network for RNA and small molecule binding sites prediction · Original source · journal full text in PMC
- RNA language model and graph attention network for RNA and small molecule binding sites prediction · Original source · journal full text in PMC
Technical metadata and extraction receipts
Stable ID: reported-task-b00a636d1ed8d9
- areas
- rna-transcriptomes
- tasks
- RNA-small-molecule binding-site prediction
- entity level
- task
- version
- Not reported
- task
- RNA-small-molecule binding-site prediction
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- benchmark research
- review date: 2026-09-17; status: primary_comparison_table_screened; primary sources: expansion-p3-rlsite-rna-binding-2025; inspected locators: Tables 1–3 footnotes; Section 2.1 Benchmark datasets; searched queries: "PMC12417085"; gaps: Most baseline values are copied from original publications; RNABind is a web-server run.; T18/T3/T10 are separate protocols and cannot be pooled as one model score.; Unavailable RNet AUC is a dash, not zero.; claim scope: Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.
- 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: rlsite-rna-binding-2025; source locator: Methods §§2.1, 2.7; cached text lines 13–15, 57–58; 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: T18
- benchmark: RLsite: RNA-small-molecule binding-site prediction