RNA-RNA and RNA-protein complexes with no chain at TM-score >= 0.7 to a pre-cut-off PDB complex (hard).
24 evaluations · 24 results. Different protocols are not a single leaderboard.
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 RNA complex hard set, mean DockQ Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 0.215 DockQ unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaFold3 on RNA complex hard set (DockQ) lit-rna-20261011-rna3d-protocol-complex-hard-mean-dockq Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'AF3', column 'DockQ' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean F1 Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 0.202 F1 (interface residues (atom within 5 A of the partner chain)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaFold3 on RNA complex hard set (F1) lit-rna-20261011-rna3d-protocol-complex-hard-mean-f1 Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'AF3', column 'F1' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean fnat Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 0.199 Fnat unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaFold3 on RNA complex hard set (fnat) lit-rna-20261011-rna3d-protocol-complex-hard-mean-fnat Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'AF3', column 'fnat' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean iRMSD Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 21.4 CAPRI interface RMSD angstrom · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaFold3 on RNA complex hard set (iRMSD) lit-rna-20261011-rna3d-protocol-complex-hard-mean-irmsd Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'AF3', column 'iRMSD' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean LRMSD Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 43.9 CAPRI ligand RMSD angstrom · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaFold3 on RNA complex hard set (LRMSD) lit-rna-20261011-rna3d-protocol-complex-hard-mean-lrmsd Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'AF3', column 'LRMSD' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean TM-score Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 0.47 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 RNA complex hard set (TM-score) lit-rna-20261011-rna3d-protocol-complex-hard-mean-tm-score Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'AF3', column 'TM-score' |
| Configuration: Boltz-1 0.4.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean DockQ Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 0.224 DockQ 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 RNA complex hard set (DockQ) lit-rna-20261011-rna3d-protocol-complex-hard-mean-dockq Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'Boltz-1', column 'DockQ' |
| Configuration: Boltz-1 0.4.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean F1 Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 0.205 F1 (interface residues (atom within 5 A of the partner chain)) 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 RNA complex hard set (F1) lit-rna-20261011-rna3d-protocol-complex-hard-mean-f1 Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'Boltz-1', column 'F1' |
| Configuration: Boltz-1 0.4.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean fnat Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 0.216 Fnat 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 RNA complex hard set (fnat) lit-rna-20261011-rna3d-protocol-complex-hard-mean-fnat Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'Boltz-1', column 'fnat' |
| Configuration: Boltz-1 0.4.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean iRMSD Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 19.6 CAPRI interface RMSD angstrom · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBoltz-1 on RNA complex hard set (iRMSD) lit-rna-20261011-rna3d-protocol-complex-hard-mean-irmsd Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'Boltz-1', column 'iRMSD' |
| Configuration: Boltz-1 0.4.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean LRMSD Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 41.2 CAPRI ligand RMSD angstrom · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBoltz-1 on RNA complex hard set (LRMSD) lit-rna-20261011-rna3d-protocol-complex-hard-mean-lrmsd Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'Boltz-1', column 'LRMSD' |
| Configuration: Boltz-1 0.4.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean TM-score Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 0.446 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 RNA complex hard set (TM-score) lit-rna-20261011-rna3d-protocol-complex-hard-mean-tm-score Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'Boltz-1', column 'TM-score' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean DockQ Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 0.165 DockQ unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHelixFold3 on RNA complex hard set (DockQ) lit-rna-20261011-rna3d-protocol-complex-hard-mean-dockq Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'HF3', column 'DockQ' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean F1 Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 0.162 F1 (interface residues (atom within 5 A of the partner chain)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHelixFold3 on RNA complex hard set (F1) lit-rna-20261011-rna3d-protocol-complex-hard-mean-f1 Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'HF3', column 'F1' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean fnat Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 0.161 Fnat unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHelixFold3 on RNA complex hard set (fnat) lit-rna-20261011-rna3d-protocol-complex-hard-mean-fnat Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'HF3', column 'fnat' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean iRMSD Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 23.3 CAPRI interface RMSD angstrom · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHelixFold3 on RNA complex hard set (iRMSD) lit-rna-20261011-rna3d-protocol-complex-hard-mean-irmsd Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'HF3', column 'iRMSD' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean LRMSD Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 48.6 CAPRI ligand RMSD angstrom · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHelixFold3 on RNA complex hard set (LRMSD) lit-rna-20261011-rna3d-protocol-complex-hard-mean-lrmsd Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'HF3', column 'LRMSD' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean TM-score Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 0.288 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 RNA complex hard set (TM-score) lit-rna-20261011-rna3d-protocol-complex-hard-mean-tm-score Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'HF3', column 'TM-score' |
| Configuration: RosettaFoldNA commit f761af2 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean DockQ Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 0.105 DockQ unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceRosettaFoldNA on RNA complex hard set (DockQ) lit-rna-20261011-rna3d-protocol-complex-hard-mean-dockq Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'RF2NA', column 'DockQ' |
| Configuration: RosettaFoldNA commit f761af2 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean F1 Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 0.135 F1 (interface residues (atom within 5 A of the partner chain)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceRosettaFoldNA on RNA complex hard set (F1) lit-rna-20261011-rna3d-protocol-complex-hard-mean-f1 Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'RF2NA', column 'F1' |
| Configuration: RosettaFoldNA commit f761af2 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean fnat Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 0.137 Fnat unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceRosettaFoldNA on RNA complex hard set (fnat) lit-rna-20261011-rna3d-protocol-complex-hard-mean-fnat Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'RF2NA', column 'fnat' |
| Configuration: RosettaFoldNA commit f761af2 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean iRMSD Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 31.5 CAPRI interface RMSD angstrom · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceRosettaFoldNA on RNA complex hard set (iRMSD) lit-rna-20261011-rna3d-protocol-complex-hard-mean-irmsd Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'RF2NA', column 'iRMSD' |
| Configuration: RosettaFoldNA commit f761af2 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean LRMSD Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 60.6 CAPRI ligand RMSD angstrom · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceRosettaFoldNA on RNA complex hard set (LRMSD) lit-rna-20261011-rna3d-protocol-complex-hard-mean-lrmsd Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'RF2NA', column 'LRMSD' |
| Configuration: RosettaFoldNA commit f761af2 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean TM-score Dataset: Ludaic and Elofsson 2026 RNA complex hard set | 0.286 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 RNA complex hard set (TM-score) lit-rna-20261011-rna3d-protocol-complex-hard-mean-tm-score Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 5, row 'RF2NA', column 'TM-score' |
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| 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 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Split Hard Context-only references | Limits of deep-learning-based RNA prediction methods 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| 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 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Description RNA-RNA and RNA-protein complexes with no chain at TM-score >= 0.7 to a pre-cut-off PDB complex (hard). Context-only references | Limits of deep-learning-based RNA prediction methods 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Name Ludaic and Elofsson 2026 RNA complex hard set Context-only references | Limits of deep-learning-based RNA prediction methods 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: lit-rna-20261011-rna3d-data-complex-hard