Method

ViennaRNA RNAfold

RNAfold predicts RNA secondary structure and thermodynamic ensemble quantities within the ViennaRNA package.

Sources

ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License

How it worksViennaRNA RNAfold workflow

Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.

Sources

ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License

At a glance

Model type

Thermodynamic RNA secondary-structure procedure

Sources

ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License

Inputs

RNA nucleotide sequence with selected thermodynamic settings and supported constraints.

Sources

ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License

Outputs

Predicted secondary structure and, in ensemble mode, partition-function-derived probabilities.

Sources

ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License

Source reviewed · Automated source review, 2026-09-16. All specifications and missing details

Evaluations and results

Release 2026-09-17-d277315f7d76 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.

No evaluations linked in this release.

How it works

RNAfold predicts RNA secondary structure and thermodynamic ensemble quantities within the ViennaRNA package. Energy-based RNA secondary-structure calculation; minimum-free-energy and partition-function modes are distinct outputs. The documented inputs are RNA nucleotide sequence with selected thermodynamic settings and supported constraints. The output consists of predicted secondary structure and, in ensemble mode, partition-function-derived probabilities.

Sources

ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License

Versions and reproducibility

RNAfold within ViennaRNA; software and energy-parameter set must be pinned. Implementation and memory dependent; the package README gives an upper representational length with an explicit large-memory caveat.

Sources

ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License

Strengths and limitations

Strengths supported by sources

Provides an interpretable thermodynamic reference for comparison with learned RNA structure methods.
Sources
ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License

Limitations and conditions

The package includes multiple programs with different tasks. RNAfold secondary structure must not be presented as three-dimensional RNA folding. Sequence length is constrained by memory and algorithmic cost.
Sources
ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License

Profile review details

Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied.

Stable record: discovery-model-viennarna-rnafold

Specifications

Inputs, training, access and other details

Explanatory profile: source reviewed · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Inputs, outputs and configuration
Property	Description and evidence
Model type	Thermodynamic RNA secondary-structure procedure Sources ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License
Architecture	Energy-based RNA secondary-structure calculation; minimum-free-energy and partition-function modes are distinct outputs. Sources ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License
Inputs	RNA nucleotide sequence with selected thermodynamic settings and supported constraints. Sources ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License
Outputs	Predicted secondary structure and, in ensemble mode, partition-function-derived probabilities. Sources ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License
Parameters	Thermodynamic parameter set and algorithm settings; not neural model parameters. Sources ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License
Known versions	RNAfold within ViennaRNA; software and energy-parameter set must be pinned. Sources ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License
Training data	Energy parameters are empirical model inputs, not a pretrained neural checkpoint. Sources ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License
Training cutoff	Inapplicable to neural pretraining; reference-database and input-data dates must be recorded for each run. · Not applicable Sources ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License
Context limits	Implementation and memory dependent; the package README gives an upper representational length with an explicit large-memory caveat. Sources ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License
Weights licence	Inapplicable to neural weights; preserve the thermodynamic parameter-file version and licence. · Not applicable Sources ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License
Access	Official project documentation and implementation: https://github.com/ViennaRNA/ViennaRNA Sources ViennaRNA/ViennaRNA: README.md · README.md: package capabilities, executable programs, Energy Parameters and License
Code licence	ViennaRNA custom permissive licence; inspect the pinned COPYING terms. Sources ViennaRNA/ViennaRNA: COPYING · COPYING: licence text
Assumptions	Not extracted or verified for this record.

Applicable tests and references

Applicability is distinct from a completed evaluation.

BEACON · Proposed association

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.

20 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
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	ViennaRNA/ViennaRNA: README.md Original source ↗ README.md: package capabilities, executable programs, Energy Parameters and License Version: 1ffec79f5e258896160f7362ced8263450f371dc Retrieved: 2026-09-16T19:46:18.166113+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `d37146b01e4273062a5230c496a9af8414ee7ef14fcd905cf415959256d59c4e` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["RNA sequence and energy settings","Secondary-structure energy calculation","Minimum-energy or ensemble mode","Structure and probabilities"] Individual claims	ViennaRNA/ViennaRNA: README.md Original source ↗ README.md: package capabilities, executable programs, Energy Parameters and License Version: 1ffec79f5e258896160f7362ced8263450f371dc Retrieved: 2026-09-16T19:46:18.166113+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `d37146b01e4273062a5230c496a9af8414ee7ef14fcd905cf415959256d59c4e` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title ViennaRNA RNAfold workflow Individual claims	ViennaRNA/ViennaRNA: README.md Original source ↗ README.md: package capabilities, executable programs, Energy Parameters and License Version: 1ffec79f5e258896160f7362ced8263450f371dc Retrieved: 2026-09-16T19:46:18.166113+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `d37146b01e4273062a5230c496a9af8414ee7ef14fcd905cf415959256d59c4e` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Model type Thermodynamic RNA secondary-structure procedure Individual claims	ViennaRNA/ViennaRNA: README.md Original source ↗ README.md: package capabilities, executable programs, Energy Parameters and License Version: 1ffec79f5e258896160f7362ced8263450f371dc Retrieved: 2026-09-16T19:46:18.166113+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `d37146b01e4273062a5230c496a9af8414ee7ef14fcd905cf415959256d59c4e` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Architecture Energy-based RNA secondary-structure calculation; minimum-free-energy and partition-function modes are distinct outputs. Individual claims	ViennaRNA/ViennaRNA: README.md Original source ↗ README.md: package capabilities, executable programs, Energy Parameters and License Version: 1ffec79f5e258896160f7362ced8263450f371dc Retrieved: 2026-09-16T19:46:18.166113+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `d37146b01e4273062a5230c496a9af8414ee7ef14fcd905cf415959256d59c4e` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Access Official project documentation and implementation: https://github.com/ViennaRNA/ViennaRNA Individual claims	ViennaRNA/ViennaRNA: README.md Original source ↗ README.md: package capabilities, executable programs, Energy Parameters and License Version: 1ffec79f5e258896160f7362ced8263450f371dc Retrieved: 2026-09-16T19:46:18.166113+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `d37146b01e4273062a5230c496a9af8414ee7ef14fcd905cf415959256d59c4e` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Code licence ViennaRNA custom permissive licence; inspect the pinned COPYING terms. Individual claims	ViennaRNA/ViennaRNA: COPYING Original source ↗ COPYING: licence text Version: 1ffec79f5e258896160f7362ced8263450f371dc Retrieved: 2026-09-16T19:46:18.166113+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.11.value` Source artifact SHA-256: `7776cce4c6155eba82ea6bcb5c108f25b9fb0f604664421bfd6da94930028d8c` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Inputs RNA nucleotide sequence with selected thermodynamic settings and supported constraints. Individual claims	ViennaRNA/ViennaRNA: README.md Original source ↗ README.md: package capabilities, executable programs, Energy Parameters and License Version: 1ffec79f5e258896160f7362ced8263450f371dc Retrieved: 2026-09-16T19:46:18.166113+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `d37146b01e4273062a5230c496a9af8414ee7ef14fcd905cf415959256d59c4e` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Outputs Predicted secondary structure and, in ensemble mode, partition-function-derived probabilities. Individual claims	ViennaRNA/ViennaRNA: README.md Original source ↗ README.md: package capabilities, executable programs, Energy Parameters and License Version: 1ffec79f5e258896160f7362ced8263450f371dc Retrieved: 2026-09-16T19:46:18.166113+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `d37146b01e4273062a5230c496a9af8414ee7ef14fcd905cf415959256d59c4e` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Parameters Thermodynamic parameter set and algorithm settings; not neural model parameters. Individual claims	ViennaRNA/ViennaRNA: README.md Original source ↗ README.md: package capabilities, executable programs, Energy Parameters and License Version: 1ffec79f5e258896160f7362ced8263450f371dc Retrieved: 2026-09-16T19:46:18.166113+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `d37146b01e4273062a5230c496a9af8414ee7ef14fcd905cf415959256d59c4e` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

All evidence (CSV)All evidence (JSONL)How to read the evidence

Sources and history

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

3 source records and release history

ViennaRNA/ViennaRNA official source · Original source · 1ffec79f5e258896160f7362ced8263450f371dc
ViennaRNA/ViennaRNA: README.md · Original source · 1ffec79f5e258896160f7362ced8263450f371dc
ViennaRNA/ViennaRNA: COPYING · Original source · 1ffec79f5e258896160f7362ced8263450f371dc

Download this release

Technical metadata and extraction receipts

Stable ID: discovery-model-viennarna-rnafold

areas: rna
access: official_source_linked
benchmark applicability: candidate; not evidence of a reported evaluation
candidate benchmark ids: discovery-benchmark-beacon
entity level: method
reported name: ViennaRNA RNAfold
version: Not reported
historical missing metadata: checkpoint: unextracted; code licence: unextracted; parameters: unextracted; training cutoff: unextracted; training data: unextracted; version: unextracted; weights licence: unextracted
metadata review scope: historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
legacy kinds: model
entity classification: review date: 2026-09-17; rationale: The cited architecture/procedure describes an algorithm, representation recipe or software toolkit, rather than a single released learned biological model. Fitted models, selected reference databases and concrete runs remain separate configurations.; source ids: evidence-official-1b2aa7207e3a05f297ab; source locator: README.md: package capabilities, executable programs, Energy Parameters and License; ambiguities: None recorded

Related records

applicable to: BEACON
model: RNA minimum-free-energy folding

Suggest a correction