AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)
AlphaFold3 run by Ludaic and Elofsson with default settings on their 2026 RNA structure benchmark.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
29 evaluations · 29 results. Different protocols are not a single leaderboard.
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.
| Tested configuration | Protocol and dataset | TM score | CAPRI interface RMSD | CAPRI ligand RMSD | DockQ | F1 (interface residues (atom within 5 A of the partner chain)) | Fnat | GDT ts | Interaction network fidelity | lDDT | Success rate (INF above the CASP16 threshold) | Success rate (lDDT above the CASP16 threshold) | Success rate (TM-score above the CASP16 threshold) | DockQ (mean per-interface DockQ, RNA-protein interfaces) | DockQ (mean per-interface DockQ, RNA-RNA interfaces) | Success rate (GDT-TS above the CASP16 threshold) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 RNA complex hard set, mean TM-score, Ludaic and Elofsson 2026 RNA complex hard set | 0.47 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 Monomeric RNA easy set, mean TM-score, Ludaic and Elofsson 2026 Monomeric RNA easy set | 0.468 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 RNA complex easy set, mean TM-score, Ludaic and Elofsson 2026 RNA complex easy set | 0.415 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 Monomeric RNA hard set, mean TM-score, Ludaic and Elofsson 2026 Monomeric RNA hard set | 0.245 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 RNA-protein interfaces, mean per-interface DockQ, Ludaic and Elofsson 2026 RNA complex set, easy and hard combined | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.281 | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 RNA-RNA interfaces, mean per-interface DockQ, Ludaic and Elofsson 2026 RNA complex set, easy and hard combined | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.406 | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 RNA complex easy set, mean DockQ, Ludaic and Elofsson 2026 RNA complex easy set | Not reported | Not reported | Not reported | 0.417 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 RNA complex easy set, mean F1, Ludaic and Elofsson 2026 RNA complex easy set | Not reported | Not reported | Not reported | Not reported | 0.393 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 RNA complex easy set, mean fnat, Ludaic and Elofsson 2026 RNA complex easy set | Not reported | Not reported | Not reported | Not reported | Not reported | 0.844 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 RNA complex easy set, mean iRMSD, Ludaic and Elofsson 2026 RNA complex easy set | Not reported | 10.5 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 RNA complex easy set, mean LRMSD, Ludaic and Elofsson 2026 RNA complex easy set | Not reported | Not reported | 22.8 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 RNA complex hard set, mean DockQ, Ludaic and Elofsson 2026 RNA complex hard set | Not reported | Not reported | Not reported | 0.215 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 RNA complex hard set, mean F1, Ludaic and Elofsson 2026 RNA complex hard set | Not reported | Not reported | Not reported | Not reported | 0.202 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 RNA complex hard set, mean fnat, Ludaic and Elofsson 2026 RNA complex hard set | Not reported | Not reported | Not reported | Not reported | Not reported | 0.199 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 RNA complex hard set, mean iRMSD, Ludaic and Elofsson 2026 RNA complex hard set | Not reported | 21.4 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 RNA complex hard set, mean LRMSD, Ludaic and Elofsson 2026 RNA complex hard set | Not reported | Not reported | 43.9 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 Monomeric RNA easy set, mean GDT-TS, Ludaic and Elofsson 2026 Monomeric RNA easy set | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.585 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 Monomeric RNA easy set, mean INF, Ludaic and Elofsson 2026 Monomeric RNA easy set | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.777 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 Monomeric RNA easy set, mean lDDT, Ludaic and Elofsson 2026 Monomeric RNA easy set | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.693 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 Monomeric RNA easy set, GDT-TS success rate, Ludaic and Elofsson 2026 Monomeric RNA easy set | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 70% |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 Monomeric RNA easy set, INF success rate, Ludaic and Elofsson 2026 Monomeric RNA easy set | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 73.3% (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 Monomeric RNA easy set, lDDT success rate, Ludaic and Elofsson 2026 Monomeric RNA easy set | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 24.1% (best in column) | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 Monomeric RNA easy set, TM-score success rate, Ludaic and Elofsson 2026 Monomeric RNA easy set | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 46.7% (best in column) | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 Monomeric RNA hard set, mean GDT-TS, Ludaic and Elofsson 2026 Monomeric RNA hard set | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.433 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 Monomeric RNA hard set, mean INF, Ludaic and Elofsson 2026 Monomeric RNA hard set | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.669 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 Monomeric RNA hard set, mean lDDT, Ludaic and Elofsson 2026 Monomeric RNA hard set | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.553 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 Monomeric RNA hard set, INF success rate, Ludaic and Elofsson 2026 Monomeric RNA hard set | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 46.9% | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 Monomeric RNA hard set, lDDT success rate, Ludaic and Elofsson 2026 Monomeric RNA hard set | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 6.38% | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation | Ludaic and Elofsson 2026 Monomeric RNA hard set, TM-score success rate, Ludaic and Elofsson 2026 Monomeric RNA hard set | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 4.08% | Not reported | Not reported | Not reported |
All 29 result rows with coverage, uncertainty and sources
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| 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 checkedMethods, coverage and sourceAlphaFold3 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 checkedMethods, coverage and sourceAlphaFold3 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: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex easy set, mean DockQ Dataset: Ludaic and Elofsson 2026 RNA complex easy set | 0.417 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 easy set (DockQ) lit-rna-20261011-rna3d-protocol-complex-easy-mean-dockq Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 4, row 'AF3', column 'DockQ' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex easy set, mean F1 Dataset: Ludaic and Elofsson 2026 RNA complex easy set | 0.393 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 easy set (F1) lit-rna-20261011-rna3d-protocol-complex-easy-mean-f1 Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 4, row 'AF3', column 'F1' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex easy set, mean fnat Dataset: Ludaic and Elofsson 2026 RNA complex easy set | 0.844 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 easy set (fnat) lit-rna-20261011-rna3d-protocol-complex-easy-mean-fnat Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 4, row 'AF3', column 'fnat' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex easy set, mean iRMSD Dataset: Ludaic and Elofsson 2026 RNA complex easy set | 10.5 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 sourceAlphaFold3 on RNA complex easy set (iRMSD) lit-rna-20261011-rna3d-protocol-complex-easy-mean-irmsd Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 4, row 'AF3', column 'iRMSD' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex easy set, mean LRMSD Dataset: Ludaic and Elofsson 2026 RNA complex easy set | 22.8 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 easy set (LRMSD) lit-rna-20261011-rna3d-protocol-complex-easy-mean-lrmsd Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 4, row 'AF3', column 'LRMSD' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 RNA complex easy set, mean TM-score Dataset: Ludaic and Elofsson 2026 RNA complex easy set | 0.415 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 easy set (TM-score) lit-rna-20261011-rna3d-protocol-complex-easy-mean-tm-score Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 4, row 'AF3', column 'TM-score' |
| 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: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, mean GDT-TS Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 0.585 GDT ts 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 (GDT-TS) lit-rna-20261011-rna3d-protocol-monomer-easy-mean-gdt-ts Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 2, row 'AF3', column 'GDT-TS' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, mean INF Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 0.777 Interaction network fidelity 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 (INF) lit-rna-20261011-rna3d-protocol-monomer-easy-mean-inf Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 2, row 'AF3', column 'INF' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, mean lDDT Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 0.693 lDDT 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 (lDDT) lit-rna-20261011-rna3d-protocol-monomer-easy-mean-lddt Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 2, row 'AF3', column 'lDDT' |
| 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: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, GDT-TS success rate Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 70% Success rate (GDT-TS above the CASP16 threshold) percent · 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 (GDT-TS, success rate) lit-rna-20261011-rna3d-protocol-monomer-easy-success-gdt-ts Aggregation: Not reported Limits of deep-learning-based RNA prediction methods: Supplementary Data; Limits of deep-learning-based RNA prediction methods · Supplementary Table S6, row 'GDT-TS', column 'AF3' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, INF success rate Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 73.3% Success rate (INF above the CASP16 threshold) percent · 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 (INF, success rate) lit-rna-20261011-rna3d-protocol-monomer-easy-success-inf Aggregation: Not reported Limits of deep-learning-based RNA prediction methods: Supplementary Data; Limits of deep-learning-based RNA prediction methods · Supplementary Table S6, row 'INF', column 'AF3' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, lDDT success rate Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 24.1% Success rate (lDDT above the CASP16 threshold) percent · 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 (lDDT, success rate) lit-rna-20261011-rna3d-protocol-monomer-easy-success-lddt Aggregation: Not reported Limits of deep-learning-based RNA prediction methods: Supplementary Data; Limits of deep-learning-based RNA prediction methods · Supplementary Table S6, row 'lDDT', column 'AF3' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA easy set, TM-score success rate Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 46.7% Success rate (TM-score above the CASP16 threshold) percent · 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, success rate) lit-rna-20261011-rna3d-protocol-monomer-easy-success-tm-score Aggregation: Not reported Limits of deep-learning-based RNA prediction methods: Supplementary Data; Limits of deep-learning-based RNA prediction methods · Supplementary Table S6, row 'TM-score', column 'AF3' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA hard set, mean GDT-TS Dataset: Ludaic and Elofsson 2026 Monomeric RNA hard set | 0.433 GDT ts 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 hard set (GDT-TS) lit-rna-20261011-rna3d-protocol-monomer-hard-mean-gdt-ts Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 3, row 'AF3', column 'GDT-TS' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA hard set, mean INF Dataset: Ludaic and Elofsson 2026 Monomeric RNA hard set | 0.669 Interaction network fidelity 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 hard set (INF) lit-rna-20261011-rna3d-protocol-monomer-hard-mean-inf Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 3, row 'AF3', column 'INF' |
| Configuration: AlphaFold3 3.0.1 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA hard set, mean lDDT Dataset: Ludaic and Elofsson 2026 Monomeric RNA hard set | 0.553 lDDT 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 hard set (lDDT) lit-rna-20261011-rna3d-protocol-monomer-hard-mean-lddt Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 3, row 'AF3', column 'lDDT' |
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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- Limits of deep-learning-based RNA prediction methods: Supplementary Data · Original source · gkag813_supplemental_file.pdf from the Europe PMC supplementary files archive for PMC13501138
- 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-config-af3-ludaic2026
- areas
- rna-transcriptomes; protein-structure
- contexts
- research
- method types
- foundation_model
- reported name
- AF3
- version
- 3.0.1
- parameters
- Default settings; one NVIDIA DGX-A100 GPU; shared MSAs (rMSA against RNAcentral and NCBI nt for RNA, MMseqs2 on the ColabFold databases for protein) supplied where the method accepts custom MSAs; five models generated with the same seed and the top-ranked model analysed (native ranking score, else mean pLDDT, else the first or only model)
- access reuse
- Not stated in the source beyond the software version; see the method's own release
- foundation model eligible
- true
- source locator
- Supplementary Table S1 row 'AlphaFold 3'; Methods 'Model generation'
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