Pipeline

ERNIE-RNA + CoBRA

CoBRA uses ERNIE-RNA residue embeddings to predict small-molecule-binding nucleotides.

Sources

CoBRA: compound binding site prediction using RNA language model · Material and methods/Dataset preparation (paragraph 1); Abstract (paragraph 1)

1 evaluation · 1 metric row

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

CoBRA: compound binding site prediction using RNA language model · Introduction (paragraph 4); Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 3)

At a glance

Model type

Learned representation pipeline; this record is the paper-specific evaluated configuration.

Sources

CoBRA: compound binding site prediction using RNA language model · Introduction (paragraph 4); Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 3)

Biological inputs

RNA nucleotide sequences

Sources

CoBRA: compound binding site prediction using RNA language model · Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 4); Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 2)

Outputs

Per-nucleotide ligand-binding predictions

Sources

CoBRA: compound binding site prediction using RNA language model · Material and methods/Dataset preparation (paragraph 1); Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 4)

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.

Evaluation setupMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
ERNIE-RNA + CoBRA: RNA compound-binding site prediction Pipeline: ERNIE-RNA + CoBRATask: RNA compound-binding site predictionDataset: CoBRA compound-binding test set ERNIE-RNA embedding with TCL focal loss Author-reported evaluation · Evaluation metadata: needs review
0.657 MCC Unit: unitless · Direction: unknown	Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported	source checkedCoBRA: compound binding site prediction using RNA language model · Table 2, ERNIE-RNA / TCL focal row, MCC column Source checking is not independent reproduction.

How it works

How the evaluated method works

A pretrained RNA encoder provides contextual nucleotide vectors to a multilayer-perceptron binary classifier. Explicit RNA coordinates or distances are not supplied to the classifier.

Sources

CoBRA: compound binding site prediction using RNA language model · Introduction (paragraph 4); Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 3)

What was evaluated

The linked evaluation record identifies ERNIE-RNA + CoBRA: RNA compound-binding site prediction. Its dataset, split, adaptation and evidence origin remain attached to the reported results.

Sources

CoBRA: compound binding site prediction using RNA language model · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-b2-cobra-rna-binding-2026

Strengths and limitations

Strengths and considerations

Provides a sequence-based option when an RNA structure is unavailable.
Sources
CoBRA: compound binding site prediction using RNA language model · Results/Comparison with other existing methods on benchmark sets (paragraph 4); Discussion (paragraph 3)

Limitations and conditions

The result measures an ERNIE-RNA-plus-classifier pipeline; structural information still influences how training labels and evaluation partitions are constructed.
Sources
CoBRA: compound binding site prediction using RNA language model · Material and methods/RNA language models (paragraph 2); Results/Overall performance comparison and model selection (paragraph 5)

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-7ad28cd57f5f5b

Specifications

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.

Inputs, outputs and configuration
Property	Description and evidence
Model type	Learned representation pipeline; this record is the paper-specific evaluated configuration. Sources CoBRA: compound binding site prediction using RNA language model · Introduction (paragraph 4); Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 3)
Architecture / procedure	A pretrained RNA encoder provides contextual nucleotide vectors to a multilayer-perceptron binary classifier. Explicit RNA coordinates or distances are not supplied to the classifier. Sources CoBRA: compound binding site prediction using RNA language model · Introduction (paragraph 4); Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 3)
Biological inputs	RNA nucleotide sequences Sources CoBRA: compound binding site prediction using RNA language model · Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 4); Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 2)
Outputs	Per-nucleotide ligand-binding predictions Sources CoBRA: compound binding site prediction using RNA language model · Material and methods/Dataset preparation (paragraph 1); Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 4)
Parameters	An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sources Sources (2) CoBRA: compound binding site prediction using RNA language model; kucm-lsbi/CoBRA README.md · Material and methods/Dataset preparation; Material and methods/Model architecture; Material and methods/RNA language models; Material and methods/Loss functions; Material and methods/Evaluation metrics; Material and methods/Laplacian-based curvature for RNA 3D structure analysis; Material and methods/Evaluating computational cost with comparison to other machine learning; Results/Comparison with other existing methods on benchmark sets; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision
Known versions / configuration	ERNIE-RNA + CoBRA is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sources Sources CoBRA: compound binding site prediction using RNA language model · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label.
Training data / fitting	TR60 and HARIBOSS RNA–ligand datasets; the study tests four independent benchmark sets and additional structure-based splits. Sources CoBRA: compound binding site prediction using RNA language model · Material and methods/Dataset preparation (paragraph 3); Material and methods/Dataset preparation (paragraph 2)
Context limits	Inputs are standardised to 161 RNA nucleotides; shorter sequences are padded and chains exceeding that limit are removed. Sources CoBRA: compound binding site prediction using RNA language model · Material and methods/Model architecture (paragraph 1); Material and methods/Dataset preparation (paragraph 2)
Access	Official study implementation and usage documentation: https://github.com/kucm-lsbi/CoBRA/blob/415fd05cabf990f28a46cc2ba651531a28f7d249/README.md. This pinned documentation revision is not automatically the evaluated weight revision. Sources kucm-lsbi/CoBRA README.md · README.md; installation, model download and usage instructions
Code licence	GNU GPL version 3 as explicitly declared by the repository (study repository code at the cited revision; this does not establish every dependency or historical checkpoint licence). Sources kucm-lsbi/CoBRA 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 sources Sources kucm-lsbi/CoBRA 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

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
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	CoBRA: compound binding site prediction using RNA language model Original source ↗ Introduction (paragraph 4); Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 3) Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558197+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `8c6a6f00f5fa5f62acf301a66e9e6fa9ef11c7a05ad9b7447d2ade2ce8eba793` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram steps ["RNA nucleotide sequences","ERNIE-RNA + CoBRA","Per-nucleotide ligand-binding predictions"] Individual claims	CoBRA: compound binding site prediction using RNA language model Original source ↗ Introduction (paragraph 4); Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 3) Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558197+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `8c6a6f00f5fa5f62acf301a66e9e6fa9ef11c7a05ad9b7447d2ade2ce8eba793` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram title Evaluated procedure (conceptual) Individual claims	CoBRA: compound binding site prediction using RNA language model Original source ↗ Introduction (paragraph 4); Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 3) Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558197+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `8c6a6f00f5fa5f62acf301a66e9e6fa9ef11c7a05ad9b7447d2ade2ce8eba793` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Model type Learned representation pipeline; this record is the paper-specific evaluated configuration. Individual claims	CoBRA: compound binding site prediction using RNA language model Original source ↗ Introduction (paragraph 4); Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 3) Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558197+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `8c6a6f00f5fa5f62acf301a66e9e6fa9ef11c7a05ad9b7447d2ade2ce8eba793` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Architecture / procedure A pretrained RNA encoder provides contextual nucleotide vectors to a multilayer-perceptron binary classifier. Explicit RNA coordinates or distances are not supplied to the classifier. Individual claims	CoBRA: compound binding site prediction using RNA language model Original source ↗ Introduction (paragraph 4); Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 3) Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558197+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `8c6a6f00f5fa5f62acf301a66e9e6fa9ef11c7a05ad9b7447d2ade2ce8eba793` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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	kucm-lsbi/CoBRA README.md Original source ↗ README.md; checkpoint/access documentation and licence scope Version: 415fd05cabf990f28a46cc2ba651531a28f7d249 Retrieved: 2026-09-16T19:54:13.479891+00:00	unreported automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `9ad9fea6b42049ca4ca3f71dd906e6d1289ef842aee14bb4241e880866003bc9` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Biological inputs RNA nucleotide sequences Individual claims	CoBRA: compound binding site prediction using RNA language model Original source ↗ Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 4); Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 2) Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558197+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `8c6a6f00f5fa5f62acf301a66e9e6fa9ef11c7a05ad9b7447d2ade2ce8eba793` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Outputs Per-nucleotide ligand-binding predictions Individual claims	CoBRA: compound binding site prediction using RNA language model Original source ↗ Material and methods/Dataset preparation (paragraph 1); Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 4) Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558197+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `8c6a6f00f5fa5f62acf301a66e9e6fa9ef11c7a05ad9b7447d2ade2ce8eba793` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims	CoBRA: compound binding site prediction using RNA language model Original source ↗ Material and methods/Dataset preparation; Material and methods/Model architecture; Material and methods/RNA language models; Material and methods/Loss functions; Material and methods/Evaluation metrics; Material and methods/Laplacian-based curvature for RNA 3D structure analysis; Material and methods/Evaluating computational cost with comparison to other machine learning; Results/Comparison with other existing methods on benchmark sets; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558197+00:00	unreported automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `8c6a6f00f5fa5f62acf301a66e9e6fa9ef11c7a05ad9b7447d2ade2ce8eba793` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims	kucm-lsbi/CoBRA README.md Original source ↗ Material and methods/Dataset preparation; Material and methods/Model architecture; Material and methods/RNA language models; Material and methods/Loss functions; Material and methods/Evaluation metrics; Material and methods/Laplacian-based curvature for RNA 3D structure analysis; Material and methods/Evaluating computational cost with comparison to other machine learning; Results/Comparison with other existing methods on benchmark sets; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 415fd05cabf990f28a46cc2ba651531a28f7d249 Retrieved: 2026-09-16T19:54:13.479891+00:00	unreported automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `9ad9fea6b42049ca4ca3f71dd906e6d1289ef842aee14bb4241e880866003bc9` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

3 source records and release history

CoBRA: compound binding site prediction using RNA language model · Original source · journal full text in PMC
kucm-lsbi/CoBRA README.md · Original source · 415fd05cabf990f28a46cc2ba651531a28f7d249
kucm-lsbi/CoBRA LICENSE · Original source · 415fd05cabf990f28a46cc2ba651531a28f7d249

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Technical metadata and extraction receipts

Stable ID: reported-model-7ad28cd57f5f5b

areas: rna-transcriptomes
entity level: method
version: not stated in table
reported name: ERNIE-RNA + CoBRA
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: cobra-rna-binding-2026; source locator: Introduction (paragraph 4); Material and methods/Laplacian-based curvature for RNA 3D structure analysis (paragraph 3) | Material and methods/Dataset preparation (paragraph 1); Abstract (paragraph 1); ambiguities: This is the paper-specific pipeline identity; unspecified component checkpoints or implementation versions are not inferred from its name.

Related records

model: ERNIE-RNA + CoBRA: RNA compound-binding site prediction

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