Datasets
No single dataset is fixed by this guide. Select a linked protocol and its versioned data release.
inapplicable
Task
RNA tertiary structure
RNA tertiary-structure evaluation compares predicted three-dimensional RNA geometry with reference structures.
Sources (2)
ml4bio/RNA-FM official source; AlphaFold 3 paper · RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targetsNo reviewed evaluations are linked here in this release. See the sources and separately identified configurations below.
Overview
Metrics
Protocol-defined structural accuracy. Atom selection, reference states and treatment of missing residues must accompany a number.
Allowed inputs
RNA sequence and permitted auxiliary information, plus a reference structure for geometric evaluation.
Sources (2)
ml4bio/RNA-FM official source; AlphaFold 3 paper · RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targetsEvaluation procedure diagram
How it worksConceptual evaluation workflow
Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol.
Sources (2)
ml4bio/RNA-FM official source; AlphaFold 3 paper · RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targetsSource reviewed · Automated source review, 2026-09-16. All specifications and missing details
Results
All evaluations
0 evaluations · 0 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
No evaluations linked in this release.
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Choosing an evaluation
Declare the target molecules and available inputs, including whether an alignment is allowed. Compare coordinates against the relevant reference state using an explicit alignment and atom-selection rule. The AlphaFold 3 paper describes a CASP15 RNA comparison; the RNA-FM project documents RhoFold as a separate complete predictor. A base RNA embedding model is not itself that evaluated pipeline.
Sources (2)
ml4bio/RNA-FM official source; AlphaFold 3 paper · RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targetsTask scope
This is a task guide, not a single versioned benchmark protocol. The connected resources provide examples or concrete procedures. A candidate method or proposed control is not evidence that an evaluation has been completed.
Sources (2)
ml4bio/RNA-FM official source; AlphaFold 3 paper · RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targetsRun instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Strengths, limitations and unresolved questions
Strengths and limitations
Strengths supported by sources
- Coordinate-level scoring tests a structural endpoint beyond nucleotide pairing or embedding quality.
Sources (2)
ml4bio/RNA-FM official source; AlphaFold 3 paper · RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets
Limitations and conditions
- Alternative conformations and incomplete experimental structures complicate reference comparison. Predictions are not a calibrated dynamic ensemble.
Sources (2)
ml4bio/RNA-FM official source; AlphaFold 3 paper · RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets
Profile review details
Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol.
Stable record: catalog-task-rna-tertiary-structureSpecifications
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.
| Property | Description and evidence |
|---|---|
| Entity type | Task guide; concrete protocol identities remain separate.Sources (2)ml4bio/RNA-FM official source; AlphaFold 3 paper · RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets |
| Datasets | No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. · Not applicableSources (2)ml4bio/RNA-FM official source; AlphaFold 3 paper · RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets |
| Organisms | No shared organism population is defined at this guide level. Record it for each selected dataset. · Not applicableSources (2)ml4bio/RNA-FM official source; AlphaFold 3 paper · RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets |
| Assays | No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. · Not applicableSources (2)ml4bio/RNA-FM official source; AlphaFold 3 paper · RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets |
| Splits | No executable split is attached to this task identity. Use the selected protocol’s split manifest. · Not applicableSources (2)ml4bio/RNA-FM official source; AlphaFold 3 paper · RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets |
| Allowed inputs | RNA sequence and permitted auxiliary information, plus a reference structure for geometric evaluation.Sources (2)ml4bio/RNA-FM official source; AlphaFold 3 paper · RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets |
| Adaptation | No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. · Not applicableSources (2)ml4bio/RNA-FM official source; AlphaFold 3 paper · RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets |
| Metrics | Protocol-defined structural accuracy. Atom selection, reference states and treatment of missing residues must accompany a number.Sources (2)ml4bio/RNA-FM official source; AlphaFold 3 paper · RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets |
| Baselines | Use complete RNA-structure predictors and their stated input information; a language-model family name alone does not identify a structural pipeline.Sources (2)ml4bio/RNA-FM official source; AlphaFold 3 paper · RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets |
Evidence
Source checking verifies the cited claim or transcription. It does not establish 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 |
|---|---|---|
| Accurate structure prediction of biomolecular interactions with AlphaFold 3 | Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256 | Read source |
Historical gaps recorded on 2026-09-17
- complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
Search and extraction details
primary protocol reviewed
Searches
- RNAfold RNA secondary structure benchmark BPfold RhoFold RNA-FM paper
Evidence locations
- AF3 Fig. 1; Extended Data Fig. 3; Supplementary Methods referenced by primary paper
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.
34 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol. Individual claims | AlphaFold 3 paper RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16 | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: primary_artifact_review |
| Diagram caption Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol. Individual claims | ml4bio/RNA-FM official source RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Diagram steps
| AlphaFold 3 paper RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16 | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: primary_artifact_review |
Diagram steps
| ml4bio/RNA-FM official source RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Conceptual evaluation workflow Individual claims | AlphaFold 3 paper RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16 | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: primary_artifact_review |
| Diagram title Conceptual evaluation workflow Individual claims | ml4bio/RNA-FM official source RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Entity type Task guide; concrete protocol identities remain separate. Individual claims | AlphaFold 3 paper RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16 | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: primary_artifact_review |
| Entity type Task guide; concrete protocol identities remain separate. Individual claims | ml4bio/RNA-FM official source RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. Individual claims | AlphaFold 3 paper RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16 | inapplicable automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: primary_artifact_review |
| Datasets No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. Individual claims | ml4bio/RNA-FM official source RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e | inapplicable automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: discovered
5 source records and release history
- RNA-FM official resource · Original source · Not reported
- RhoFold+ official resource · Original source · Not reported
- Accurate structure prediction of biomolecular interactions with AlphaFold 3 · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
- ml4bio/RNA-FM official source · Original source · 348951516e0963d22bbb33b3c9fc18c89081d38e
- AlphaFold 3 paper · Original source · Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16
Technical metadata and extraction receipts
Stable ID: catalog-task-rna-tertiary-structure
- areas
- rna-transcriptomes
- entity level
- task
- version
- Not reported
- task
- RNA tertiary structure
- scope note
- Compare predicted 3D folds against independently held-out structures.
- benchmark research
- review date: 2026-09-17; status: primary_protocol_reviewed; primary sources: evidence-expansion-alphafold3-e627083f; inspected locators: AF3 Fig. 1; Extended Data Fig. 3; Supplementary Methods referenced by primary paper; searched queries: RNAfold RNA secondary structure benchmark BPfold RhoFold RNA-FM paper; gaps: complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.; 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.
- historical missing metadata
- protocol version: not_yet_extracted
- 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
- benchmark
- entity classification
- review date: 2026-09-17; rationale: This record identifies the biological prediction question or a suite-specific task, rather than a uniquely fixed evaluated procedure. Preserve its task identity and leave split, model adaptation and scoring details on linked protocols/evaluations.; source ids: src-discovery-ml4bio-rna-fm; evidence-alphafold-paper; source locator: RNA-FM README: RhoFold; AlphaFold 3 Methods: Nucleic acid prediction baseline and CASP15 RNA targets; ambiguities: None recorded