Limits of deep-learning-based RNA prediction methods: Supplementary Data
gkag813_supplemental_file.pdf from the Europe PMC supplementary files archive for PMC13501138 · Peer-reviewed
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Results
Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.
Models, benchmarks and other records
Configurations (10)
- AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)
- Boltz-1 0.4.1 (Ludaic and Elofsson 2026 RNA benchmark run)
- Chai-1 0.6.1 (Ludaic and Elofsson 2026 RNA benchmark run)
- DeepFoldRNA 1.0 (Ludaic and Elofsson 2026 RNA benchmark run)
- DRfold commit pre-release-4-g9586990 (Ludaic and Elofsson 2026 RNA benchmark run)
- HelixFold3 HelixFold3/73cd80b-hpc1 (Ludaic and Elofsson 2026 RNA benchmark run)
- NuFold commit 169a618 (Ludaic and Elofsson 2026 RNA benchmark run)
- RhoFold+ 0.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)
- RosettaFoldNA commit f761af2 (Ludaic and Elofsson 2026 RNA benchmark run)
- trRosettaRNA 1.0 (Ludaic and Elofsson 2026 RNA benchmark run)
Protocols (10)
- Ludaic and Elofsson 2026 Monomeric RNA easy set, GDT-TS success rate
- Ludaic and Elofsson 2026 Monomeric RNA easy set, INF success rate
- Ludaic and Elofsson 2026 Monomeric RNA easy set, lDDT success rate
- Ludaic and Elofsson 2026 Monomeric RNA easy set, TM-score success rate
- Ludaic and Elofsson 2026 Monomeric RNA hard set, GDT-TS success rate
- Ludaic and Elofsson 2026 Monomeric RNA hard set, INF success rate
- Ludaic and Elofsson 2026 Monomeric RNA hard set, lDDT success rate
- Ludaic and Elofsson 2026 Monomeric RNA hard set, TM-score success rate
- Ludaic and Elofsson 2026 RNA-protein interfaces, mean per-interface DockQ
- Ludaic and Elofsson 2026 RNA-RNA interfaces, mean per-interface DockQ
Evaluations (88)
- AlphaFold3 on Monomeric RNA easy set (GDT-TS, success rate)
- AlphaFold3 on Monomeric RNA easy set (INF, success rate)
- AlphaFold3 on Monomeric RNA easy set (lDDT, success rate)
- AlphaFold3 on Monomeric RNA easy set (TM-score, success rate)
- AlphaFold3 on Monomeric RNA hard set (GDT-TS, success rate)
- AlphaFold3 on Monomeric RNA hard set (INF, success rate)
- AlphaFold3 on Monomeric RNA hard set (lDDT, success rate)
- AlphaFold3 on Monomeric RNA hard set (TM-score, success rate)
- AlphaFold3 on RNA complex set, easy and hard combined (RNA-protein)
- AlphaFold3 on RNA complex set, easy and hard combined (RNA-RNA)
- Boltz-1 on Monomeric RNA easy set (GDT-TS, success rate)
- Boltz-1 on Monomeric RNA easy set (INF, success rate)
- Boltz-1 on Monomeric RNA easy set (lDDT, success rate)
- Boltz-1 on Monomeric RNA easy set (TM-score, success rate)
- Boltz-1 on Monomeric RNA hard set (GDT-TS, success rate)
- Boltz-1 on Monomeric RNA hard set (INF, success rate)
- Boltz-1 on Monomeric RNA hard set (lDDT, success rate)
- Boltz-1 on Monomeric RNA hard set (TM-score, success rate)
- Boltz-1 on RNA complex set, easy and hard combined (RNA-protein)
- Boltz-1 on RNA complex set, easy and hard combined (RNA-RNA)
- Chai-1 on Monomeric RNA easy set (GDT-TS, success rate)
- Chai-1 on Monomeric RNA easy set (INF, success rate)
- Chai-1 on Monomeric RNA easy set (lDDT, success rate)
- Chai-1 on Monomeric RNA easy set (TM-score, success rate)
- Chai-1 on Monomeric RNA hard set (GDT-TS, success rate)
Evidence
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Evidence table
Inspect claims, sources and review details
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18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.artifact_sha256 0e26a301a5b5c39a0e2dfaa092760d6099345dcb9e0545e23b730374f39d463c Source metadata | Limits of deep-learning-based RNA prediction methods: Supplementary Data No field-specific location recorded Version: gkag813_supplemental_file.pdf from the Europe PMC supplementary files archive for PMC13501138 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13501138/supplementaryFiles Source metadata | Limits of deep-learning-based RNA prediction methods: Supplementary Data No field-specific location recorded Version: gkag813_supplemental_file.pdf from the Europe PMC supplementary files archive for PMC13501138 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Doi 10.1093/nar/gkag813 Source metadata | Limits of deep-learning-based RNA prediction methods: Supplementary Data No field-specific location recorded Version: gkag813_supplemental_file.pdf from the Europe PMC supplementary files archive for PMC13501138 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Licence CC-BY-4.0 Source metadata | Limits of deep-learning-based RNA prediction methods: Supplementary Data No field-specific location recorded Version: gkag813_supplemental_file.pdf from the Europe PMC supplementary files archive for PMC13501138 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Limitations2 values
| Limits of deep-learning-based RNA prediction methods: Supplementary Data No field-specific location recorded Version: gkag813_supplemental_file.pdf from the Europe PMC supplementary files archive for PMC13501138 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Media type application/pdf Source metadata | Limits of deep-learning-based RNA prediction methods: Supplementary Data No field-specific location recorded Version: gkag813_supplemental_file.pdf from the Europe PMC supplementary files archive for PMC13501138 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Publication status peer_reviewed Source metadata | Limits of deep-learning-based RNA prediction methods: Supplementary Data No field-specific location recorded Version: gkag813_supplemental_file.pdf from the Europe PMC supplementary files archive for PMC13501138 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Retrieved at 2026-10-11T21:28:04Z Source metadata | Limits of deep-learning-based RNA prediction methods: Supplementary Data No field-specific location recorded Version: gkag813_supplemental_file.pdf from the Europe PMC supplementary files archive for PMC13501138 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Url https://doi.org/10.1093/nar/gkag813 Source metadata | Limits of deep-learning-based RNA prediction methods: Supplementary Data No field-specific location recorded Version: gkag813_supplemental_file.pdf from the Europe PMC supplementary files archive for PMC13501138 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Version gkag813_supplemental_file.pdf from the Europe PMC supplementary files archive for PMC13501138 Source metadata | Limits of deep-learning-based RNA prediction methods: Supplementary Data No field-specific location recorded Version: gkag813_supplemental_file.pdf from the Europe PMC supplementary files archive for PMC13501138 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Primary source retrieved and hashed for the 2026-10-11 RNA and other-omics literature pass.
Technical metadata and extraction receipts
Stable ID: lit-rna-20261011-rna3d-source-ludaic2026-supplement
- areas
- rna-transcriptomes; protein-structure
- contexts
- research
- url
- https://doi.org/10.1093/nar/gkag813
- artifact url
- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13501138/supplementaryFiles
- version
- gkag813_supplemental_file.pdf from the Europe PMC supplementary files archive for PMC13501138
- retrieved at
- 2026-10-11T21:28:04Z
- artifact sha256
- 0e26a301a5b5c39a0e2dfaa092760d6099345dcb9e0545e23b730374f39d463c
- doi
- 10.1093/nar/gkag813
- publication status
- peer_reviewed
- licence
- CC-BY-4.0
- media type
- application/pdf
- limitations
- Read through the pdftotext -layout text layer; values were transcribed from the text layer, not from page renders.; Supplementary Table S7 prints 37.78% for AF3 GDT-TS on the hard set; Supplementary Table S4 gives 19 of 49 targets (38.78%). The DRfold and DeepFoldRNA per-target INF, GDT-TS and lDDT columns of Supplementary Tables S3-S5 are identical.