Configuration

SimFold

SimFold as evaluated in the cited study. MultiRNAFold 2.0 in RNAsoft; default parameters

Sources

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 11 SimFold, 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: SimFold	Protocol: PDB (RNA secondary structure) Dataset: PDB RNA set	0.739 INF unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SimFold: 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 11 SimFold, column 6: PDB INF
Configuration: SimFold	Protocol: ArchiveII (RNA secondary structure) Dataset: ArchiveII	0.568 F1 unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SimFold: 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 11 SimFold, column 7: ArchiveII F1
Configuration: SimFold	Protocol: Rfam12.3–14.10 (RNA secondary structure) Dataset: Rfam12.3–14.10	0.646 INF unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SimFold: 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 11 SimFold, column 2: Rfam12.3–14.10 INF
Configuration: SimFold	Protocol: bpRNA-TS0 (RNA secondary structure) Dataset: bpRNA-TS0	0.52 INF unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SimFold: 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 11 SimFold, column 2: bpRNA-TS0 INF
Configuration: SimFold	Protocol: bpRNA-TS0 (RNA secondary structure) Dataset: bpRNA-TS0	0.626 Recall unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SimFold: 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 11 SimFold, column 5: bpRNA-TS0 Recall
Configuration: SimFold	Protocol: Rfam12.3–14.10 (RNA secondary structure) Dataset: Rfam12.3–14.10	0.639 F1 unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SimFold: 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 11 SimFold, column 3: Rfam12.3–14.10 F1
Configuration: SimFold	Protocol: PDB (RNA secondary structure) Dataset: PDB RNA set	0.714 Recall unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SimFold: 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 11 SimFold, column 9: PDB Recall
Configuration: SimFold	Protocol: ArchiveII (RNA secondary structure) Dataset: ArchiveII	0.55 Precision unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SimFold: 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 11 SimFold, column 8: ArchiveII Precision
Configuration: SimFold	Protocol: Rfam12.3–14.10 (RNA secondary structure) Dataset: Rfam12.3–14.10	0.593 Precision unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SimFold: 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 11 SimFold, column 4: Rfam12.3–14.10 Precision
Configuration: SimFold	Protocol: bpRNA-TS0 (RNA secondary structure) Dataset: bpRNA-TS0	0.507 F1 unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SimFold: 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 11 SimFold, column 3: bpRNA-TS0 F1
Configuration: SimFold	Protocol: Rfam12.3–14.10 (RNA secondary structure) Dataset: Rfam12.3–14.10	0.713 Recall unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SimFold: 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 11 SimFold, column 5: Rfam12.3–14.10 Recall
Configuration: SimFold	Protocol: ArchiveII (RNA secondary structure) Dataset: ArchiveII	0.594 Recall unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SimFold: 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 11 SimFold, column 9: ArchiveII Recall
Configuration: SimFold	Protocol: bpRNA-TS0 (RNA secondary structure) Dataset: bpRNA-TS0	0.448 Precision unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SimFold: 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 11 SimFold, column 4: bpRNA-TS0 Precision
Configuration: SimFold	Protocol: PDB (RNA secondary structure) Dataset: PDB RNA set	0.77 Precision unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SimFold: 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 11 SimFold, column 8: PDB Precision
Configuration: SimFold	Protocol: ArchiveII (RNA secondary structure) Dataset: ArchiveII	0.57 INF unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SimFold: 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 11 SimFold, column 6: ArchiveII INF
Configuration: SimFold	Protocol: PDB (RNA secondary structure) Dataset: PDB RNA set	0.736 F1 unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SimFold: 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 11 SimFold, column 7: PDB F1

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

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Evaluation in this paper

MultiRNAFold 2.0 in RNAsoft; default parameters

Sources

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 11 SimFold, column 2: bpRNA-TS0 INF

Strengths, limitations and unresolved questions

Strengths and limitations

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Stable record: paper-model-9635867dc1fe6fbefc

Specifications

Inputs, training, access and other details

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.

Inputs, outputs and configuration
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Evidence

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Evidence table

Inspect claims, sources and review details

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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 MultiRNAFold 2.0 in RNAsoft; default parameters Individual claims	Deep generalizable prediction of RNA secondary structure via base pair motif energy Original source ↗ Table 1 (Tab1), row 11 SimFold, 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 SimFold as evaluated in the cited study. MultiRNAFold 2.0 in RNAsoft; default parameters Individual claims	Deep generalizable prediction of RNA secondary structure via base pair motif energy Original source ↗ Table 1 (Tab1), row 11 SimFold, 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-9635867dc1fe6fbefc

areas: rna-transcriptomes
tasks: RNA secondary structure
entity level: method
configuration type: reported_configuration
version: MultiRNAFold 2.0 in RNAsoft; default parameters
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 11 SimFold, 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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