Protocol

PDB (RNA secondary structure)

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

Sources

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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB INF

10 evaluations · 40 metric rows

At a glance

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.

Data, procedure and scoring
Property	Description and evidence
Datasets	Not extracted or verified for this record.
Organisms	Not extracted or verified for this record.
Assays	Not extracted or verified for this record.
Splits	Not extracted or verified for this record.
Allowed inputs	Not extracted or verified for this record.
Adaptation	Not extracted or verified for this record.
Metrics	Not extracted or verified for this record.
Baselines	Not extracted or verified for this record.

How it works

Evaluation in this paper

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

Sources

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

PDB · INF

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

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

Evaluation protocol · PDB RNA set

BPfold · Configuration · Author-reported evaluation0.817
SPOT-RNA · Configuration · Independent external evaluation0.814
MXfold2 · Configuration · Independent external evaluation0.782
ContextFold · Configuration · Independent external evaluation0.743
CONTRAfold · Configuration · Independent external evaluation0.754
EternaFold · Configuration · Independent external evaluation0.760
LinearFold · Configuration · Independent external evaluation0.726
RNAfold · Configuration · Independent external evaluation0.749
SimFold · Configuration · Independent external evaluation0.739
RNAstructure · Configuration · Independent external evaluation0.754

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	0.817 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 6: PDB INF
SPOT-RNA · Configuration	0.814 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 6: PDB INF
MXfold2 · Configuration	0.782 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 6: PDB INF
ContextFold · Configuration	0.743 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 6: PDB INF
CONTRAfold · Configuration	0.754 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 6: PDB INF
EternaFold · Configuration	0.760 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 6: PDB INF
LinearFold · Configuration	0.726 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 6: PDB INF
RNAfold · Configuration	0.749 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 6: PDB INF
SimFold · Configuration	0.739 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 6: PDB INF
RNAstructure · Configuration	0.754 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 6: PDB 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
BPfold: RNA secondary structure Configuration: BPfoldProtocol: PDB (RNA secondary structure)Dataset: PDB RNA set Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Author-reported evaluation · Evaluation metadata: needs review
0.814 F1 Unit: unitless · Direction: higher	Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2, BPfold row, PDB F1 column Source checking is not independent reproduction.
0.801 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 9: PDB Recall Source checking is not independent reproduction.
0.840 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 8: PDB Precision Source checking is not independent reproduction.
0.817 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 3 BPfold, column 6: PDB INF Source checking is not independent reproduction.
RNAfold: RNA secondary structure Configuration: RNAfoldProtocol: 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
0.747 F1 Unit: unitless · Direction: higher	Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2, RNAfold row, PDB F1 column Source checking is not independent reproduction.
0.776 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 10 RNAfold, column 8: PDB Precision Source checking is not independent reproduction.
0.728 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 9: PDB Recall Source checking is not independent reproduction.
MXfold2: PDB Configuration: MXfold2Protocol: 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
0.733 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 9: PDB Recall Source checking is not independent reproduction.
0.777 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 7: PDB F1 Source checking is not independent reproduction.
CONTRAfold: PDB Configuration: CONTRAfoldProtocol: 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
0.708 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 9: PDB Recall Source checking is not independent reproduction.
0.754 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 6: PDB INF Source checking is not independent reproduction.
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.
SPOT-RNA: PDB Configuration: SPOT-RNAProtocol: 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
0.772 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 4 SPOT-RNA, column 9: PDB Recall Source checking is not independent reproduction.
0.814 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 4 SPOT-RNA, column 6: PDB INF Source checking is not independent reproduction.
0.808 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 7: PDB F1 Source checking is not independent reproduction.
EternaFold: PDB Configuration: EternaFoldProtocol: 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
0.760 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 6: PDB INF Source checking is not independent reproduction.
0.785 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 8 EternaFold, column 8: PDB Precision Source checking is not independent reproduction.
0.758 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 7: PDB F1 Source checking is not independent reproduction.
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 8 EternaFold, column 9: PDB Recall Source checking is not independent reproduction.
ContextFold: PDB Configuration: ContextFoldProtocol: 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
0.737 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 7: PDB F1 Source checking is not independent reproduction.
0.795 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 8: PDB Precision Source checking is not independent reproduction.
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 6 ContextFold, column 9: PDB Recall Source checking is not independent reproduction.
LinearFold: PDB Configuration: LinearFoldProtocol: 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
0.726 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 9 LinearFold, column 6: PDB INF Source checking is not independent reproduction.
0.672 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 9: PDB Recall Source checking is not independent reproduction.
0.718 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 9 LinearFold, column 7: PDB 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB 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-b8acf180ccd3e67923

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.

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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB 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 PDB · 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB 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-4ed991b8a49690f09d 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB 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-9e3711f962442d3019 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

1 source records and release history

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-b8acf180ccd3e67923

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-pdb-inf; title: PDB · INF; protocol id: paper-protocol-b8acf180ccd3e67923; dataset id: reported-dataset-8317793f18b026; metric: INF; unit: unitless; direction: higher; result ids: paper-result-97b54396c089187bac; paper-result-5465552e8e451ecd56; paper-result-e465e8b97a72acc635; paper-result-d1041275466a1cb1ae; paper-result-3d0a9108d41aebb9db; paper-result-3ddc4380f7d4e8cc34; paper-result-738dbc58785cabadb7; paper-result-c2cbc18894bd07f1a6; paper-result-155bc3cd1981f1e9fd; paper-result-cfbfd2a82ace58ed84; 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB 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-pdb-f1; title: PDB · F1; protocol id: paper-protocol-b8acf180ccd3e67923; dataset id: reported-dataset-8317793f18b026; metric: F1; unit: unitless; direction: higher; result ids: lit-011; paper-result-57c0ff7b77a652ab1c; paper-result-3d2877af386639e0ad; paper-result-4ae34e1cc310c60554; paper-result-b6a3c4b03b40732ef2; paper-result-96d2c93b67543eaa47; paper-result-9440f5e0b35b26980b; lit-012; paper-result-fda0f45ba9232f7233; paper-result-c35bfeb0f7fc67fda6; 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 7: PDB F1; Table 2 (Tab2), row 4 SPOT-RNA, column 7: PDB F1; Table 2 (Tab2), row 5 MXfold2, column 7: PDB F1; Table 2 (Tab2), row 6 ContextFold, column 7: PDB F1; Table 2 (Tab2), row 7 CONTRAfold, column 7: PDB F1; Table 2 (Tab2), row 8 EternaFold, column 7: PDB F1; Table 2 (Tab2), row 9 LinearFold, column 7: PDB F1; Table 2 (Tab2), row 10 RNAfold, column 7: PDB F1; Table 2 (Tab2), row 11 SimFold, column 7: PDB F1; Table 2 (Tab2), row 12 RNAstructure, column 7: PDB 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-pdb-precision; title: PDB · Precision; protocol id: paper-protocol-b8acf180ccd3e67923; dataset id: reported-dataset-8317793f18b026; metric: Precision; unit: unitless; direction: higher; result ids: paper-result-8319fb26cf3f85d194; paper-result-eac4aa84532a86e39b; paper-result-b6a55e179b51c6398e; paper-result-5ae72ffe6dc5e67fcd; paper-result-d4877662e8f67af294; paper-result-49bafa3b1c623a5f8d; paper-result-c96dd6eb50a381f576; paper-result-2d080d038082cd24e2; paper-result-ddafb4472501414293; paper-result-c9d2c92f2b018f5062; 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 8: PDB Precision; Table 2 (Tab2), row 4 SPOT-RNA, column 8: PDB Precision; Table 2 (Tab2), row 5 MXfold2, column 8: PDB Precision; Table 2 (Tab2), row 6 ContextFold, column 8: PDB Precision; Table 2 (Tab2), row 7 CONTRAfold, column 8: PDB Precision; Table 2 (Tab2), row 8 EternaFold, column 8: PDB Precision; Table 2 (Tab2), row 9 LinearFold, column 8: PDB Precision; Table 2 (Tab2), row 10 RNAfold, column 8: PDB Precision; Table 2 (Tab2), row 11 SimFold, column 8: PDB Precision; Table 2 (Tab2), row 12 RNAstructure, column 8: PDB 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-pdb-recall; title: PDB · Recall; protocol id: paper-protocol-b8acf180ccd3e67923; dataset id: reported-dataset-8317793f18b026; metric: Recall; unit: unitless; direction: higher; result ids: paper-result-5afb76a439dd9677b9; paper-result-3ad0144bc78eae6759; paper-result-01efc77bc3fe0c8593; paper-result-5fe58d35cc68e79078; paper-result-11126a2ff54dbf3afb; paper-result-a45e9b5b53f964bd93; paper-result-8828c8e20f56d3d354; paper-result-6f6f94f1d2e661baac; paper-result-a7667b03bef3a87b94; paper-result-c0cf50ee8c90573ad2; 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 9: PDB Recall; Table 2 (Tab2), row 4 SPOT-RNA, column 9: PDB Recall; Table 2 (Tab2), row 5 MXfold2, column 9: PDB Recall; Table 2 (Tab2), row 6 ContextFold, column 9: PDB Recall; Table 2 (Tab2), row 7 CONTRAfold, column 9: PDB Recall; Table 2 (Tab2), row 8 EternaFold, column 9: PDB Recall; Table 2 (Tab2), row 9 LinearFold, column 9: PDB Recall; Table 2 (Tab2), row 10 RNAfold, column 9: PDB Recall; Table 2 (Tab2), row 11 SimFold, column 9: PDB Recall; Table 2 (Tab2), row 12 RNAstructure, column 9: PDB 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB INF; ambiguities: None recorded

Related records

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

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