Protocol

Rfam12.3–14.10 (RNA secondary structure)

Rfam12.3–14.10 · INF. Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF

10 evaluations · 40 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

Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Tasks

These source-backed links do not make different protocols or scores interchangeable.

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Published comparisons

Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies.

Comparison and metric

Rfam12.3–14.10 · INF

INF (unitless) · Higher values are better for this metric.

Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Evaluation protocol · Rfam12.3–14.10

BPfold · Configuration · Author-reported evaluation0.694
SPOT-RNA · Configuration · Independent external evaluation0.678
MXfold2 · Configuration · Independent external evaluation0.670
ContextFold · Configuration · Independent external evaluation0.616
CONTRAfold · Configuration · Independent external evaluation0.667
EternaFold · Configuration · Independent external evaluation0.672
LinearFold · Configuration · Independent external evaluation0.654
RNAfold · Configuration · Independent external evaluation0.656
SimFold · Configuration · Independent external evaluation0.646
RNAstructure · Configuration · Independent external evaluation0.651

Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.

Values, uncertainty and evidence

INF: original source values
Tested entity	Printed value	Uncertainty	Evidence
BPfold · Configuration	0.694 unitless	Not reported	Author-reported evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF
SPOT-RNA · Configuration	0.678 unitless	Not reported	Independent external evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF
MXfold2 · Configuration	0.670 unitless	Not reported	Independent external evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF
ContextFold · Configuration	0.616 unitless	Not reported	Independent external evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF
CONTRAfold · Configuration	0.667 unitless	Not reported	Independent external evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF
EternaFold · Configuration	0.672 unitless	Not reported	Independent external evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF
LinearFold · Configuration	0.654 unitless	Not reported	Independent external evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF
RNAfold · Configuration	0.656 unitless	Not reported	Independent external evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF
SimFold · Configuration	0.646 unitless	Not reported	Independent external evaluation · 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
RNAstructure · Configuration	0.651 unitless	Not reported	Independent external evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF

Scope and limitations

Within each dataset and metric only. Distinct training data, thermodynamic priors and learned methods are retained; dataset size is not a base-pair denominator. These are BPfold-author evaluations of external methods, not Rewire reproductions. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.

Source transcription and grouping reviewed by automated source review on 2026-09-17. These experiments were not independently reproduced by rewire.

Tested entities and results

Release 2026-09-17-d277315f7d76 · 10 evaluations · 40 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
MXfold2: Rfam12.3–14.10 Configuration: MXfold2Protocol: 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
0.632 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 5 MXfold2, column 4: Rfam12.3–14.10 Precision Source checking is not independent reproduction.
0.664 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 5 MXfold2, column 3: Rfam12.3–14.10 F1 Source checking is not independent reproduction.
0.670 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 5 MXfold2, column 2: Rfam12.3–14.10 INF Source checking is not independent reproduction.
0.720 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 5 MXfold2, column 5: Rfam12.3–14.10 Recall Source checking is not independent reproduction.
CONTRAfold: Rfam12.3–14.10 Configuration: CONTRAfoldProtocol: 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
0.702 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 7 CONTRAfold, column 5: Rfam12.3–14.10 Recall Source checking is not independent reproduction.
0.667 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 7 CONTRAfold, column 2: Rfam12.3–14.10 INF Source checking is not independent reproduction.
0.660 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 7 CONTRAfold, column 3: Rfam12.3–14.10 F1 Source checking is not independent reproduction.
SPOT-RNA: Rfam12.3–14.10 Configuration: SPOT-RNAProtocol: 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
0.678 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 4 SPOT-RNA, column 4: Rfam12.3–14.10 Precision Source checking is not independent reproduction.
0.672 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 4 SPOT-RNA, column 3: Rfam12.3–14.10 F1 Source checking is not independent reproduction.
EternaFold: Rfam12.3–14.10 Configuration: EternaFoldProtocol: 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
0.672 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 8 EternaFold, column 2: Rfam12.3–14.10 INF Source checking is not independent reproduction.
0.664 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 8 EternaFold, column 3: Rfam12.3–14.10 F1 Source checking is not independent reproduction.
RNAfold: Rfam12.3–14.10 Configuration: RNAfoldProtocol: 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
0.729 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 10 RNAfold, column 5: Rfam12.3–14.10 Recall Source checking is not independent reproduction.
0.649 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 10 RNAfold, column 3: Rfam12.3–14.10 F1 Source checking is not independent reproduction.
RNAstructure: Rfam12.3–14.10 Configuration: RNAstructureProtocol: 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
0.643 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 12 RNAstructure, column 3: Rfam12.3–14.10 F1 Source checking is not independent reproduction.
0.651 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 12 RNAstructure, column 2: Rfam12.3–14.10 INF Source checking is not independent reproduction.
0.724 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 12 RNAstructure, column 5: Rfam12.3–14.10 Recall Source checking is not independent reproduction.
BPfold: Rfam12.3–14.10 Configuration: BPfoldProtocol: Rfam12.3–14.10 (RNA secondary structure)Dataset: Rfam12.3–14.10 Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Author-reported evaluation · Evaluation metadata: needs review
0.741 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 3 BPfold, column 5: Rfam12.3–14.10 Recall Source checking is not independent reproduction.
0.660 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 3 BPfold, column 4: Rfam12.3–14.10 Precision Source checking is not independent reproduction.
ContextFold: Rfam12.3–14.10 Configuration: ContextFoldProtocol: 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
0.595 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 6 ContextFold, column 4: Rfam12.3–14.10 Precision Source checking is not independent reproduction.
0.648 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 6 ContextFold, column 5: Rfam12.3–14.10 Recall Source checking is not independent reproduction.
0.612 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 6 ContextFold, column 3: Rfam12.3–14.10 F1 Source checking is not independent reproduction.
LinearFold: Rfam12.3–14.10 Configuration: LinearFoldProtocol: 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
0.669 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 9 LinearFold, column 5: Rfam12.3–14.10 Recall Source checking is not independent reproduction.
0.677 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 9 LinearFold, column 4: Rfam12.3–14.10 Precision 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.

Papers and result coverage

Last literature check: 2026-09-17. Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.

Paper or primary resource	Version	Reference
Deep generalizable prediction of RNA secondary structure via base pair motif energy	version of record	Read source DOI: 10.1038/s41467-025-60048-1

What is still missing

exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.

Search and extraction details

complete tables extracted

Searches

Deep generalizable prediction of RNA secondary structure via base pair motif energy 10.1038/s41467-025-60048-1

Evidence locations

Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF

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-protocol-4c3af10c18f615709d

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.

4 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 Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Individual claims	Deep generalizable prediction of RNA secondary structure via base pair motif energy Original source ↗ Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 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 Rfam12.3–14.10 · INF. Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Individual claims	Deep generalizable prediction of RNA secondary structure via base pair motif energy Original source ↗ Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 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
Relationship: evaluates task catalog-task-rna-secondary-structure Individual claims	Deep generalizable prediction of RNA secondary structure via base pair motif energy Original source ↗ Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	source checked automated source review · 2026-09-17 Audit details Field: `links:evaluates_task:catalog-task-rna-secondary-structure` Claim: paper-claim-36bdaefda28a560679 Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: evaluates task reported-task-dc82fcbfb44935 Individual claims	Deep generalizable prediction of RNA secondary structure via base pair motif energy Original source ↗ Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	source checked automated source review · 2026-09-17 Audit details Field: `links:evaluates_task:reported-task-dc82fcbfb44935` Claim: paper-claim-68edd9d3431250a26a 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-protocol-4c3af10c18f615709d

areas: rna-transcriptomes
tasks: RNA secondary structure
entity level: protocol
protocol: Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.
comparison panels: id: bpfold-2025-tab2-rfam12-3-14-10-inf; title: Rfam12.3–14.10 · INF; protocol id: paper-protocol-4c3af10c18f615709d; dataset id: paper-dataset-816ebb930725137655; metric: INF; unit: unitless; direction: higher; result ids: paper-result-bc33c532295af7b251; paper-result-d3521184aa90f4092f; paper-result-625df7ddcc5441ab69; paper-result-ae0e3455f6b89e6f70; paper-result-57fc7701f0c9da77d0; paper-result-26e74e5c77ce1570a9; paper-result-ad4f1a6205fecd1b6d; paper-result-d197148a19effcf018; paper-result-68b0000887cc4b5e80; paper-result-853e1b3f8354ef0290; source ids: bpfold-2025; source locator: Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF; context: Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.; caveats: Within each dataset and metric only. Distinct training data, thermodynamic priors and learned methods are retained; dataset size is not a base-pair denominator. These are BPfold-author evaluations of external methods, not Rewire reproductions. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17; id: bpfold-2025-tab2-rfam12-3-14-10-f1; title: Rfam12.3–14.10 · F1; protocol id: paper-protocol-4c3af10c18f615709d; dataset id: paper-dataset-816ebb930725137655; metric: F1; unit: unitless; direction: higher; result ids: paper-result-d8fb52a660fba363da; paper-result-3019f81982dc6332cf; paper-result-0ce94efc1ed30c3769; paper-result-a34fce1d750df98700; paper-result-ac79fb8c90b25f7318; paper-result-3db670da1582c96f89; paper-result-f60a9b4fba0bdd5bca; paper-result-5c3a3c43a76fcaeb84; paper-result-7f0004110bb610598b; paper-result-31c527dabf4e1f6958; source ids: bpfold-2025; source locator: Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 4 SPOT-RNA, column 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 5 MXfold2, column 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 6 ContextFold, column 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 7 CONTRAfold, column 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 8 EternaFold, column 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 9 LinearFold, column 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 10 RNAfold, column 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 11 SimFold, column 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 12 RNAstructure, column 3: Rfam12.3–14.10 F1; context: Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.; caveats: Within each dataset and metric only. Distinct training data, thermodynamic priors and learned methods are retained; dataset size is not a base-pair denominator. These are BPfold-author evaluations of external methods, not Rewire reproductions. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17; id: bpfold-2025-tab2-rfam12-3-14-10-precision; title: Rfam12.3–14.10 · Precision; protocol id: paper-protocol-4c3af10c18f615709d; dataset id: paper-dataset-816ebb930725137655; metric: Precision; unit: unitless; direction: higher; result ids: paper-result-4c05190191ba52c1d1; paper-result-22774caf06553a0120; paper-result-03b61894f52b9f6a21; paper-result-39a55efc7440a14e65; paper-result-c859a2ad30d5982c35; paper-result-d49a44e7ee0390f25d; paper-result-6e6c7831c443afa6ed; paper-result-e59816ecb58e31617e; paper-result-b6a697b1154c255641; paper-result-f3fb35d7219cc3367e; source ids: bpfold-2025; source locator: Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 4 SPOT-RNA, column 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 5 MXfold2, column 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 6 ContextFold, column 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 7 CONTRAfold, column 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 8 EternaFold, column 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 9 LinearFold, column 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 10 RNAfold, column 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 11 SimFold, column 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 12 RNAstructure, column 4: Rfam12.3–14.10 Precision; context: Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.; caveats: Within each dataset and metric only. Distinct training data, thermodynamic priors and learned methods are retained; dataset size is not a base-pair denominator. These are BPfold-author evaluations of external methods, not Rewire reproductions. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17; id: bpfold-2025-tab2-rfam12-3-14-10-recall; title: Rfam12.3–14.10 · Recall; protocol id: paper-protocol-4c3af10c18f615709d; dataset id: paper-dataset-816ebb930725137655; metric: Recall; unit: unitless; direction: higher; result ids: paper-result-399712a182e4786639; paper-result-c824c3c83e5e451637; paper-result-a1f081e3b661ff4c25; paper-result-99b4cc2229fcdd0626; paper-result-0c3b54bf620bf11af3; paper-result-b94255fbaa7ff64d55; paper-result-453956286dc654a2fc; paper-result-30d6b97036164e9290; paper-result-c7d3e722ba9b016c03; paper-result-975ccfae7d5107a44a; source ids: bpfold-2025; source locator: Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 4 SPOT-RNA, column 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 5 MXfold2, column 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 6 ContextFold, column 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 7 CONTRAfold, column 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 8 EternaFold, column 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 9 LinearFold, column 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 10 RNAfold, column 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 11 SimFold, column 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 12 RNAstructure, column 5: Rfam12.3–14.10 Recall; context: Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.; caveats: Within each dataset and metric only. Distinct training data, thermodynamic priors and learned methods are retained; dataset size is not a base-pair denominator. These are BPfold-author evaluations of external methods, not Rewire reproductions. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17
benchmark research: review date: 2026-09-17; status: complete_tables_extracted; primary sources: bpfold-2025; inspected locators: Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF; searched queries: Deep generalizable prediction of RNA secondary structure via base pair motif energy 10.1038/s41467-025-60048-1; gaps: exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.; claim scope: Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
legacy kinds: benchmark
entity classification: review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: bpfold-2025; source locator: Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF; ambiguities: None recorded

Related records

evaluates task: RNA secondary structure
evaluates task: RNA secondary structure
subject: Rfam12.3–14.10 (RNA secondary structure): links:evaluates_task:catalog-task-rna-secondary-structure
subject: Rfam12.3–14.10 (RNA secondary structure): links:evaluates_task:reported-task-dc82fcbfb44935
benchmark: RNAstructure: Rfam12.3–14.10
benchmark: RNAfold: Rfam12.3–14.10
benchmark: MXfold2: Rfam12.3–14.10
benchmark: LinearFold: Rfam12.3–14.10
benchmark: EternaFold: Rfam12.3–14.10
benchmark: SPOT-RNA: Rfam12.3–14.10
benchmark: SimFold: Rfam12.3–14.10
benchmark: CONTRAfold: Rfam12.3–14.10
benchmark: BPfold: Rfam12.3–14.10
benchmark: ContextFold: Rfam12.3–14.10

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