Configuration

SimFold

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

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 metric rows

At a glance

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.

How it works

Evaluation in this paper

MultiRNAFold 2.0 in RNAsoft; default parameters

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

Evaluations and results

Release 2026-09-17-d277315f7d76 · 4 evaluations · 16 metric rows. Different protocols are not a single leaderboard.

Evaluation setupMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
SimFold: PDB Configuration: SimFoldProtocol: PDB (RNA secondary structure)Dataset: PDB RNA set Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Independent external evaluation · Evaluation metadata: needs review
0.739 INF Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 11 SimFold, column 6: PDB INF Source checking is not independent reproduction.
0.714 Recall Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 11 SimFold, column 9: PDB Recall Source checking is not independent reproduction.
0.770 Precision Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 11 SimFold, column 8: PDB Precision Source checking is not independent reproduction.
0.736 F1 Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep 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.
SimFold: ArchiveII Configuration: SimFoldProtocol: ArchiveII (RNA secondary structure)Dataset: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Independent external evaluation · Evaluation metadata: needs review
0.568 F1 Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 11 SimFold, column 7: ArchiveII F1 Source checking is not independent reproduction.
0.550 Precision Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 11 SimFold, column 8: ArchiveII Precision Source checking is not independent reproduction.
0.594 Recall Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 11 SimFold, column 9: ArchiveII Recall Source checking is not independent reproduction.
0.570 INF Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 11 SimFold, column 6: ArchiveII INF Source checking is not independent reproduction.
SimFold: Rfam12.3–14.10 Configuration: SimFoldProtocol: Rfam12.3–14.10 (RNA secondary structure)Dataset: Rfam12.3–14.10 Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Independent external evaluation · Evaluation metadata: needs review
0.646 INF Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF Source checking is not independent reproduction.
0.639 F1 Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 11 SimFold, column 3: Rfam12.3–14.10 F1 Source checking is not independent reproduction.
0.593 Precision Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 11 SimFold, column 4: Rfam12.3–14.10 Precision Source checking is not independent reproduction.
0.713 Recall Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 11 SimFold, column 5: Rfam12.3–14.10 Recall Source checking is not independent reproduction.
SimFold: bpRNA-TS0 Configuration: SimFoldProtocol: bpRNA-TS0 (RNA secondary structure)Dataset: bpRNA-TS0 Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Independent external evaluation · Evaluation metadata: needs review
0.520 INF Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 11 SimFold, column 2: bpRNA-TS0 INF Source checking is not independent reproduction.
0.626 Recall Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 11 SimFold, column 5: bpRNA-TS0 Recall Source checking is not independent reproduction.
0.507 F1 Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 11 SimFold, column 3: bpRNA-TS0 F1 Source checking is not independent reproduction.
0.448 Precision Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 11 SimFold, column 4: bpRNA-TS0 Precision Source checking is not independent reproduction.

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

No source-reviewed explanatory claims are recorded here yet.

Profile review details

Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.

Stable record: paper-model-9635867dc1fe6fbefc

Evidence table

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.

2 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
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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Sources and history

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

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Original source · version of record

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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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