Configuration

CONTRAfold

CONTRAfold as evaluated in the cited study. version 2.02

Sources

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF

4 evaluations · 16 results

Overview

Key specifications have not been extracted for this record. See the linked evaluation and sources for the reported setup.

limited source coverage · Automated source review, 2026-09-17. All specifications and missing details

Evaluations and results

4 evaluations · 16 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CONTRAfold	Protocol: Rfam12.3–14.10 (RNA secondary structure) Dataset: Rfam12.3–14.10	0.702 Recall unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONTRAfold: Rfam12.3–14.10 Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 7 CONTRAfold, column 5: Rfam12.3–14.10 Recall
Configuration: CONTRAfold	Protocol: bpRNA-TS0 (RNA secondary structure) Dataset: bpRNA-TS0	0.557 INF unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONTRAfold: bpRNA-TS0 Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF
Configuration: CONTRAfold	Protocol: PDB (RNA secondary structure) Dataset: PDB RNA set	0.708 Recall unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONTRAfold: PDB Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 7 CONTRAfold, column 9: PDB Recall
Configuration: CONTRAfold	Protocol: PDB (RNA secondary structure) Dataset: PDB RNA set	0.754 INF unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONTRAfold: PDB Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF
Configuration: CONTRAfold	Protocol: ArchiveII (RNA secondary structure) Dataset: ArchiveII	0.594 F1 unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONTRAfold: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 7 CONTRAfold, column 7: ArchiveII F1
Configuration: CONTRAfold	Protocol: ArchiveII (RNA secondary structure) Dataset: ArchiveII	0.588 Recall unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONTRAfold: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 7 CONTRAfold, column 9: ArchiveII Recall
Configuration: CONTRAfold	Protocol: Rfam12.3–14.10 (RNA secondary structure) Dataset: Rfam12.3–14.10	0.667 INF unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONTRAfold: Rfam12.3–14.10 Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF
Configuration: CONTRAfold	Protocol: bpRNA-TS0 (RNA secondary structure) Dataset: bpRNA-TS0	0.547 F1 unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONTRAfold: bpRNA-TS0 Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 7 CONTRAfold, column 3: bpRNA-TS0 F1
Configuration: CONTRAfold	Protocol: ArchiveII (RNA secondary structure) Dataset: ArchiveII	0.612 Precision unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONTRAfold: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 7 CONTRAfold, column 8: ArchiveII Precision
Configuration: CONTRAfold	Protocol: bpRNA-TS0 (RNA secondary structure) Dataset: bpRNA-TS0	0.625 Recall unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONTRAfold: bpRNA-TS0 Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 7 CONTRAfold, column 5: bpRNA-TS0 Recall
Configuration: CONTRAfold	Protocol: Rfam12.3–14.10 (RNA secondary structure) Dataset: Rfam12.3–14.10	0.66 F1 unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONTRAfold: Rfam12.3–14.10 Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 7 CONTRAfold, column 3: Rfam12.3–14.10 F1
Configuration: CONTRAfold	Protocol: PDB (RNA secondary structure) Dataset: PDB RNA set	0.748 F1 unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONTRAfold: PDB Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 7 CONTRAfold, column 7: PDB F1
Configuration: CONTRAfold	Protocol: Rfam12.3–14.10 (RNA secondary structure) Dataset: Rfam12.3–14.10	0.648 Precision unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONTRAfold: Rfam12.3–14.10 Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 7 CONTRAfold, column 4: Rfam12.3–14.10 Precision
Configuration: CONTRAfold	Protocol: PDB (RNA secondary structure) Dataset: PDB RNA set	0.819 Precision unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONTRAfold: PDB Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 7 CONTRAfold, column 8: PDB Precision
Configuration: CONTRAfold	Protocol: bpRNA-TS0 (RNA secondary structure) Dataset: bpRNA-TS0	0.515 Precision unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONTRAfold: bpRNA-TS0 Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 7 CONTRAfold, column 4: bpRNA-TS0 Precision
Configuration: CONTRAfold	Protocol: ArchiveII (RNA secondary structure) Dataset: ArchiveII	0.597 INF unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONTRAfold: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 7 CONTRAfold, column 6: ArchiveII INF

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version 2.02

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Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF

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Stable record: paper-model-543bc77b87a08dad52

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Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

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Evidence

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2 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
Evaluation in this paper version 2.02 Individual claims	Deep generalizable prediction of RNA secondary structure via base pair motif energy Original source ↗ Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.sections.0.body` Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Introduction CONTRAfold as evaluated in the cited study. version 2.02 Individual claims	Deep generalizable prediction of RNA secondary structure via base pair motif energy Original source ↗ Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.summary` Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Technical metadata and extraction receipts

Stable ID: paper-model-543bc77b87a08dad52

areas: rna-transcriptomes
tasks: RNA secondary structure
entity level: method
configuration type: reported_configuration
version: version 2.02
legacy kinds: model
entity classification: review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: bpfold-2025; source locator: Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF; ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.

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