Dataset

Ludaic and Elofsson 2026 RNA complex set, easy and hard combined

All 158 RNA complex structures, easy and hard sets processed together for the per-interface DockQ analysis.

Evaluation results

8 evaluations · 8 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
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 RNA-protein interfaces, mean per-interface DockQ Dataset: Ludaic and Elofsson 2026 RNA complex set, easy and hard combined	0.281 DockQ (mean per-interface DockQ, RNA-protein interfaces) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaFold3 on RNA complex set, easy and hard combined (RNA-protein) lit-rna-20261011-rna3d-protocol-complex-all-if-rna-protein Aggregation: Not reported Limits of deep-learning-based RNA prediction methods: Supplementary Data; Limits of deep-learning-based RNA prediction methods · Supplementary Table S15, row 'RNA-protein', column 'AF3'
Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)	Protocol: Ludaic and Elofsson 2026 RNA-RNA interfaces, mean per-interface DockQ Dataset: Ludaic and Elofsson 2026 RNA complex set, easy and hard combined	0.406 DockQ (mean per-interface DockQ, RNA-RNA interfaces) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaFold3 on RNA complex set, easy and hard combined (RNA-RNA) lit-rna-20261011-rna3d-protocol-complex-all-if-rna-rna Aggregation: Not reported Limits of deep-learning-based RNA prediction methods: Supplementary Data; Limits of deep-learning-based RNA prediction methods · Supplementary Table S15, row 'RNA-RNA', column 'AF3'
Configuration: Boltz-1 0.4.1 (Ludaic and Elofsson 2026 RNA benchmark run)	Protocol: Ludaic and Elofsson 2026 RNA-protein interfaces, mean per-interface DockQ Dataset: Ludaic and Elofsson 2026 RNA complex set, easy and hard combined	0.256 DockQ (mean per-interface DockQ, RNA-protein interfaces) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz-1 on RNA complex set, easy and hard combined (RNA-protein) lit-rna-20261011-rna3d-protocol-complex-all-if-rna-protein Aggregation: Not reported Limits of deep-learning-based RNA prediction methods: Supplementary Data; Limits of deep-learning-based RNA prediction methods · Supplementary Table S15, row 'RNA-protein', column 'Boltz-1'
Configuration: Boltz-1 0.4.1 (Ludaic and Elofsson 2026 RNA benchmark run)	Protocol: Ludaic and Elofsson 2026 RNA-RNA interfaces, mean per-interface DockQ Dataset: Ludaic and Elofsson 2026 RNA complex set, easy and hard combined	0.42 DockQ (mean per-interface DockQ, RNA-RNA interfaces) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz-1 on RNA complex set, easy and hard combined (RNA-RNA) lit-rna-20261011-rna3d-protocol-complex-all-if-rna-rna Aggregation: Not reported Limits of deep-learning-based RNA prediction methods: Supplementary Data; Limits of deep-learning-based RNA prediction methods · Supplementary Table S15, row 'RNA-RNA', column 'Boltz-1'
Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (Ludaic and Elofsson 2026 RNA benchmark run)	Protocol: Ludaic and Elofsson 2026 RNA-protein interfaces, mean per-interface DockQ Dataset: Ludaic and Elofsson 2026 RNA complex set, easy and hard combined	0.075 DockQ (mean per-interface DockQ, RNA-protein interfaces) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HelixFold3 on RNA complex set, easy and hard combined (RNA-protein) lit-rna-20261011-rna3d-protocol-complex-all-if-rna-protein Aggregation: Not reported Limits of deep-learning-based RNA prediction methods: Supplementary Data; Limits of deep-learning-based RNA prediction methods · Supplementary Table S15, row 'RNA-protein', column 'HF3'
Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (Ludaic and Elofsson 2026 RNA benchmark run)	Protocol: Ludaic and Elofsson 2026 RNA-RNA interfaces, mean per-interface DockQ Dataset: Ludaic and Elofsson 2026 RNA complex set, easy and hard combined	0.373 DockQ (mean per-interface DockQ, RNA-RNA interfaces) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HelixFold3 on RNA complex set, easy and hard combined (RNA-RNA) lit-rna-20261011-rna3d-protocol-complex-all-if-rna-rna Aggregation: Not reported Limits of deep-learning-based RNA prediction methods: Supplementary Data; Limits of deep-learning-based RNA prediction methods · Supplementary Table S15, row 'RNA-RNA', column 'HF3'
Configuration: RosettaFoldNA commit f761af2 (Ludaic and Elofsson 2026 RNA benchmark run)	Protocol: Ludaic and Elofsson 2026 RNA-protein interfaces, mean per-interface DockQ Dataset: Ludaic and Elofsson 2026 RNA complex set, easy and hard combined	0.039 DockQ (mean per-interface DockQ, RNA-protein interfaces) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RosettaFoldNA on RNA complex set, easy and hard combined (RNA-protein) lit-rna-20261011-rna3d-protocol-complex-all-if-rna-protein Aggregation: Not reported Limits of deep-learning-based RNA prediction methods: Supplementary Data; Limits of deep-learning-based RNA prediction methods · Supplementary Table S15, row 'RNA-protein', column 'RF2NA'
Configuration: RosettaFoldNA commit f761af2 (Ludaic and Elofsson 2026 RNA benchmark run)	Protocol: Ludaic and Elofsson 2026 RNA-RNA interfaces, mean per-interface DockQ Dataset: Ludaic and Elofsson 2026 RNA complex set, easy and hard combined	0.138 DockQ (mean per-interface DockQ, RNA-RNA interfaces) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RosettaFoldNA on RNA complex set, easy and hard combined (RNA-RNA) lit-rna-20261011-rna3d-protocol-complex-all-if-rna-rna Aggregation: Not reported Limits of deep-learning-based RNA prediction methods: Supplementary Data; Limits of deep-learning-based RNA prediction methods · Supplementary Table S15, row 'RNA-RNA', column 'RF2NA'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

Evidence incomplete

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Dataset and evaluation context

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Evidence

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Evidence table

Inspect claims, sources and review details

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5 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Source location Methods 'Benchmark dataset'; Results 'Performance of structure prediction methods on monomeric RNAs' and '... RNA complexes' Context-only references	Limits of deep-learning-based RNA prediction methods Original source ↗ Methods 'Benchmark dataset'; Results 'Performance of structure prediction methods on monomeric RNAs' and '... RNA complexes' Version: Nucleic Acids Research 2026, gkag813 (issue date 2026-08-01); PMC13501138 full-text XML Retrieved: 2026-10-11T21:27:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `02043b4a3edbb62101f6abbca56c896a63fa5c7dc0c3956c58164daff015ad1f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split Easy and hard combined Context-only references	Limits of deep-learning-based RNA prediction methods Original source ↗ Methods 'Benchmark dataset'; Results 'Performance of structure prediction methods on monomeric RNAs' and '... RNA complexes' Version: Nucleic Acids Research 2026, gkag813 (issue date 2026-08-01); PMC13501138 full-text XML Retrieved: 2026-10-11T21:27:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `02043b4a3edbb62101f6abbca56c896a63fa5c7dc0c3956c58164daff015ad1f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Version PDB entries released after the training cut-offs, downloaded January 2026, plus CASP16 RNA targets Context-only references	Limits of deep-learning-based RNA prediction methods Original source ↗ Methods 'Benchmark dataset'; Results 'Performance of structure prediction methods on monomeric RNAs' and '... RNA complexes' Version: Nucleic Acids Research 2026, gkag813 (issue date 2026-08-01); PMC13501138 full-text XML Retrieved: 2026-10-11T21:27:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `02043b4a3edbb62101f6abbca56c896a63fa5c7dc0c3956c58164daff015ad1f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description All 158 RNA complex structures, easy and hard sets processed together for the per-interface DockQ analysis. Context-only references	Limits of deep-learning-based RNA prediction methods Original source ↗ Methods 'Benchmark dataset'; Results 'Performance of structure prediction methods on monomeric RNAs' and '... RNA complexes' Version: Nucleic Acids Research 2026, gkag813 (issue date 2026-08-01); PMC13501138 full-text XML Retrieved: 2026-10-11T21:27:03Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `02043b4a3edbb62101f6abbca56c896a63fa5c7dc0c3956c58164daff015ad1f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Name Ludaic and Elofsson 2026 RNA complex set, easy and hard combined Context-only references	Limits of deep-learning-based RNA prediction methods Original source ↗ Methods 'Benchmark dataset'; Results 'Performance of structure prediction methods on monomeric RNAs' and '... RNA complexes' Version: Nucleic Acids Research 2026, gkag813 (issue date 2026-08-01); PMC13501138 full-text XML Retrieved: 2026-10-11T21:27:03Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `02043b4a3edbb62101f6abbca56c896a63fa5c7dc0c3956c58164daff015ad1f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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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

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Technical metadata and extraction receipts

Stable ID: lit-rna-20261011-rna3d-data-complex-all

areas: rna-transcriptomes; protein-structure
contexts: research
version: PDB entries released after the training cut-offs, downloaded January 2026, plus CASP16 RNA targets
split: Easy and hard combined
source locator: Methods 'Benchmark dataset'; Results 'Performance of structure prediction methods on monomeric RNAs' and '... RNA complexes'

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