Ludaic and Elofsson 2026 Monomeric RNA easy set, mean TM-score
Top-ranked model per target scored against the experimental structure (trimmed to resolved residues); mean TM-score over the monomeric rna easy set.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
10 recorded evaluations, 10 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
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All evaluations
10 evaluations · 10 results. Different protocols are not a single leaderboard.
Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, mean TM-score · Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set
Sorted by TM score (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
All 10 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, mean TM-score Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 0.468 TM score unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaFold3 on Monomeric RNA easy set (TM-score) lit-rna-20261011-rna3d-protocol-monomer-easy-mean-tm-score Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 2, row 'AF3', column 'TM-score' |
| Configuration: Boltz-1 0.4.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, mean TM-score Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 0.461 TM score unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBoltz-1 on Monomeric RNA easy set (TM-score) lit-rna-20261011-rna3d-protocol-monomer-easy-mean-tm-score Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 2, row 'Boltz-1', column 'TM-score' |
| Configuration: Chai-1 0.6.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, mean TM-score Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 0.402 TM score unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceChai-1 on Monomeric RNA easy set (TM-score) lit-rna-20261011-rna3d-protocol-monomer-easy-mean-tm-score Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 2, row 'Chai', column 'TM-score' |
| Configuration: DeepFoldRNA 1.0 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, mean TM-score Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 0.428 TM score unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDeepFoldRNA on Monomeric RNA easy set (TM-score) lit-rna-20261011-rna3d-protocol-monomer-easy-mean-tm-score Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 2, row 'DeepFoldRNA', column 'TM-score' |
| Configuration: DRfold commit pre-release-4-g9586990 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, mean TM-score Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 0.458 TM score unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDRfold on Monomeric RNA easy set (TM-score) lit-rna-20261011-rna3d-protocol-monomer-easy-mean-tm-score Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 2, row 'DRfold', column 'TM-score' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, mean TM-score Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 0.381 TM score unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHelixFold3 on Monomeric RNA easy set (TM-score) lit-rna-20261011-rna3d-protocol-monomer-easy-mean-tm-score Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 2, row 'HF3', column 'TM-score' |
| Configuration: NuFold commit 169a618 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, mean TM-score Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 0.482 TM score unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNuFold on Monomeric RNA easy set (TM-score) lit-rna-20261011-rna3d-protocol-monomer-easy-mean-tm-score Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 2, row 'NuFold', column 'TM-score' |
| Configuration: RosettaFoldNA commit f761af2 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, mean TM-score Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 0.408 TM score unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceRosettaFoldNA on Monomeric RNA easy set (TM-score) lit-rna-20261011-rna3d-protocol-monomer-easy-mean-tm-score Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 2, row 'RF2NA', column 'TM-score' |
| Configuration: RhoFold+ 0.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, mean TM-score Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 0.377 TM score unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceRhoFold+ on Monomeric RNA easy set (TM-score) lit-rna-20261011-rna3d-protocol-monomer-easy-mean-tm-score Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 2, row 'RhoFold+', column 'TM-score' |
| Configuration: trRosettaRNA 1.0 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, mean TM-score Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 0.342 TM score unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcetrRosettaRNA on Monomeric RNA easy set (TM-score) lit-rna-20261011-rna3d-protocol-monomer-easy-mean-tm-score Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 2, row 'trRosettaRNA', column 'TM-score' |
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- AlphaFold3 on Monomeric RNA easy set (TM-score)
- Boltz-1 on Monomeric RNA easy set (TM-score)
- Chai-1 on Monomeric RNA easy set (TM-score)
- DeepFoldRNA on Monomeric RNA easy set (TM-score)
- DRfold on Monomeric RNA easy set (TM-score)
- HelixFold3 on Monomeric RNA easy set (TM-score)
- NuFold on Monomeric RNA easy set (TM-score)
- RosettaFoldNA on Monomeric RNA easy set (TM-score)
- RhoFold+ on Monomeric RNA easy set (TM-score)
- trRosettaRNA on Monomeric RNA easy set (TM-score)
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
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- External evaluations
- 10
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Null control
Proposed control: requires review
Protocol-valid structural control
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Thermodynamic folding with protocol-compatible input constraints
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- Limits of deep-learning-based RNA prediction methods · Original source · Nucleic Acids Research 2026, gkag813 (issue date 2026-08-01); PMC13501138 full-text XML
Technical metadata and extraction receipts
Stable ID: lit-rna-20261011-rna3d-protocol-monomer-easy-mean-tm-score
- areas
- rna-transcriptomes; protein-structure
- contexts
- research
- protocol
- Top-ranked model per target scored against the experimental structure (trimmed to resolved residues); mean TM-score over the monomeric rna easy set
- version
- Ludaic and Elofsson 2026
- metric
- tm-score
- metric direction
- higher
- unit
- unitless
- source locator
- Tables 2-5; Methods 'Model evaluation'
- limitations
- Independent benchmark; the authors developed none of the methods.; Easy and hard are defined by structural similarity to the PDB training data and differ for monomers and complexes.
- metric implementation
- RNA-align TM-score for monomers; US-align TM-score (-mm 1 -ter 0) for complexes
Related records
- part of: Ludaic and Elofsson 2026 RNA structure benchmark
- uses data: Ludaic and Elofsson 2026 Monomeric RNA easy set
- assessment: AlphaFold3 on Monomeric RNA easy set (TM-score)
- assessment: Boltz-1 on Monomeric RNA easy set (TM-score)
- assessment: Chai-1 on Monomeric RNA easy set (TM-score)
- assessment: DeepFoldRNA on Monomeric RNA easy set (TM-score)
- assessment: DRfold on Monomeric RNA easy set (TM-score)
- assessment: HelixFold3 on Monomeric RNA easy set (TM-score)
- assessment: NuFold on Monomeric RNA easy set (TM-score)
- assessment: RosettaFoldNA on Monomeric RNA easy set (TM-score)
- assessment: RhoFold+ on Monomeric RNA easy set (TM-score)
- assessment: trRosettaRNA on Monomeric RNA easy set (TM-score)