Datasets
HARIBOSS and TR60 training resources, with RB9, JL10, TL12 and TE18 reserved for testing.
Task
RNA compound-binding site prediction
RNA compound-binding prediction is evaluated at nucleotide level with independent test collections and a structural-generalization check.
Sources
CoBRA: compound binding site prediction using RNA language model · Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65Overview
Metrics
Precision, recall, F1, MCC, AUROC and AUPRC.
Allowed inputs
RNA sequence only; explicit RNA structures are not required for CoBRA inference.
Sources
CoBRA: compound binding site prediction using RNA language model · Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65Evaluation procedure diagram
How it worksComputational evaluation flow
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Sources
CoBRA: compound binding site prediction using RNA language model · Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
1 evaluation · 1 result. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Pipeline: ERNIE-RNA + CoBRA | Task: RNA compound-binding site prediction Dataset: CoBRA compound-binding test set | 0.657 MCC unitless · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceERNIE-RNA + CoBRA: RNA compound-binding site prediction ERNIE-RNA embedding with TCL focal loss Aggregation: Not reported CoBRA: compound binding site prediction using RNA language model · Table 2, ERNIE-RNA / TCL focal row, MCC column |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Evaluation methodology
HARIBOSS and TR60 training resources, with RB9, JL10, TL12 and TE18 reserved for testing. Combined HARIBOSS/TR60 data use an 80:10:10 internal partition; RB9, JL10, TL12 and TE18 remain external tests. RNABind structural splits define an additional retraining setting. Precision, recall, F1, MCC, AUROC and AUPRC. Comparisons include RNABind and other structure-aware methods in the structural-split evaluation. Sequences overlapping training and the four external tests are removed; structural-split retraining separately tests structure-level generalization.
Sources
CoBRA: compound binding site prediction using RNA language model · Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65Recorded evaluations
Each evaluation records what was tested and under which conditions.
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Strengths, limitations and unresolved questions
Strengths and limitations
Strengths and considerations
- Sequence-overlap removal protects the external tests; a separate structural-split experiment probes a different generalization boundary.
Sources
CoBRA: compound binding site prediction using RNA language model · Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65
Limitations and conditions
- Metal and nonmetal compounds are both present. Sequence-only and structure-aware comparators use different input information.
Sources
CoBRA: compound binding site prediction using RNA language model · Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65
Profile review details
Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change.
Stable record: reported-task-3a3bff34cce634Specifications
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 | HARIBOSS and TR60 training resources, with RB9, JL10, TL12 and TE18 reserved for testing.SourcesCoBRA: compound binding site prediction using RNA language model · Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 |
| Splits | Combined HARIBOSS/TR60 data use an 80:10:10 internal partition; RB9, JL10, TL12 and TE18 remain external tests. RNABind structural splits define an additional retraining setting.SourcesCoBRA: compound binding site prediction using RNA language model · Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 |
| Metrics | Precision, recall, F1, MCC, AUROC and AUPRC.SourcesCoBRA: compound binding site prediction using RNA language model · Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 |
| Baselines | Comparisons include RNABind and other structure-aware methods in the structural-split evaluation.SourcesCoBRA: compound binding site prediction using RNA language model · Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 |
| Leakage controls | Sequences overlapping training and the four external tests are removed; structural-split retraining separately tests structure-level generalization.SourcesCoBRA: compound binding site prediction using RNA language model · Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 |
| 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 sourcesSourcesCoBRA: compound binding site prediction using RNA language model · Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 |
| Entity type | Paper-specific computational evaluation protocol.SourcesCoBRA: compound binding site prediction using RNA language model · Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 |
| Organisms | The evaluation pools PDB-derived RNA–ligand complexes from HARIBOSS, TR60, RB9, TL12, JL10 and TE18. Dataset preparation filters ligands, chain length and overlapping sequences, but does not enumerate the organism composition of each resulting subset. · Not reported in inspected sourcesSourcesCoBRA: compound binding site prediction using RNA language model · Material and methods: Dataset preparation |
| Assays | RNA compound-binding-site annotations.SourcesCoBRA: compound binding site prediction using RNA language model · Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 |
| Allowed inputs | RNA sequence only; explicit RNA structures are not required for CoBRA inference.SourcesCoBRA: compound binding site prediction using RNA language model · Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 |
| Adaptation | Frozen RNA-model residue embeddings feed a supervised MLP; language-model parameters are not updated.SourcesCoBRA: compound binding site prediction using RNA language model · Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 |
Evidence
Source checking verifies the cited claim or transcription. It does not establish 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 |
|---|---|---|
| CoBRA: compound binding site prediction using RNA language model | journal full text in PMC | Read source DOI: 10.1093/bib/bbaf713 |
Historical gaps recorded on 2026-09-17
The catalogue now holds 1 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.
- Baselines in Table 4 are taken from Gao et al., Zhu et al. and Chen et al.; this is a literature comparison, not uniformly rerun methods.
- Do not assign the selected CoBRA pipeline score to RiNALMo alone; absent values are unavailable, not zero.
Search and extraction details
primary comparison table screened
Searches
- "COBRA" "RNA" "PMC12790621"
Evidence locations
- Table 4 footnote
- Results: Comparison with other existing methods on benchmark sets
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.
18 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 | CoBRA: compound binding site prediction using RNA language model Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Diagram steps
| CoBRA: compound binding site prediction using RNA language model Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | CoBRA: compound binding site prediction using RNA language model Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets HARIBOSS and TR60 training resources, with RB9, JL10, TL12 and TE18 reserved for testing. Individual claims | CoBRA: compound binding site prediction using RNA language model Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits Combined HARIBOSS/TR60 data use an 80:10:10 internal partition; RB9, JL10, TL12 and TE18 remain external tests. RNABind structural splits define an additional retraining setting. Individual claims | CoBRA: compound binding site prediction using RNA language model Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Frozen RNA-model residue embeddings feed a supervised MLP; language-model parameters are not updated. Individual claims | CoBRA: compound binding site prediction using RNA language model Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics Precision, recall, F1, MCC, AUROC and AUPRC. Individual claims | CoBRA: compound binding site prediction using RNA language model Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines Comparisons include RNABind and other structure-aware methods in the structural-split evaluation. Individual claims | CoBRA: compound binding site prediction using RNA language model Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls Sequences overlapping training and the four external tests are removed; structural-split retraining separately tests structure-level generalization. Individual claims | CoBRA: compound binding site prediction using RNA language model Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. 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 | CoBRA: compound binding site prediction using RNA language model Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65 Version: journal full text in PMC | unreported automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
2 source records and release history
- CoBRA: compound binding site prediction using RNA language model · Original source · journal full text in PMC
- CoBRA: compound binding site prediction using RNA language model · Original source · journal full text in PMC
Technical metadata and extraction receipts
Stable ID: reported-task-3a3bff34cce634
- areas
- rna-transcriptomes
- tasks
- RNA compound-binding site prediction
- entity level
- task
- version
- Not reported
- task
- RNA compound-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-cobra-rna-binding-2026; inspected locators: Table 4 footnote; Results: Comparison with other existing methods on benchmark sets; searched queries: "COBRA" "RNA" "PMC12790621"; gaps: Baselines in Table 4 are taken from Gao et al., Zhu et al. and Chen et al.; this is a literature comparison, not uniformly rerun methods.; Do not assign the selected CoBRA pipeline score to RiNALMo alone; absent values are unavailable, 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: cobra-rna-binding-2026; source locator: Methods: Dataset preparation; Evaluation metrics; Results: Structure-based split dataset evaluation; cached text lines 9–13, 35–36, 61–65; 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.