HelixFold3 HelixFold3/73cd80b-hpc1 (Ludaic and Elofsson 2026 RNA benchmark run)
HelixFold3 run by Ludaic and Elofsson with default settings on their 2026 RNA structure benchmark.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
30 evaluations · 30 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.
All 30 result rows with coverage, uncertainty and sources
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| 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 checkedMethods, coverage and sourceHelixFold3 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 checkedMethods, coverage and sourceHelixFold3 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: HelixFold3 HelixFold3/73cd80b-hpc1 (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 | 0.173 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 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 'HF3', column 'DockQ' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (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 | 0.108 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 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 'HF3', column 'F1' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (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 | 0.448 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 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 'HF3', column 'fnat' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (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 | 21.1 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 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 'HF3', column 'iRMSD' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (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 | 43.5 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 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 'HF3', column 'LRMSD' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (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 | 0.108 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 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 'HF3', 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: HelixFold3 HelixFold3/73cd80b-hpc1 (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 | 0.512 GDT ts 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 (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 'HF3', column 'GDT-TS' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (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 | 0.758 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 sourceHelixFold3 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 'HF3', column 'INF' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (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 | 0.61 lDDT 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 (lDDT) lit-rna-20261011-rna3d-protocol-monomer-easy-mean-lddt Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 2, row 'HF3', column 'lDDT' |
| 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: HelixFold3 HelixFold3/73cd80b-hpc1 (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 | 60% 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 sourceHelixFold3 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 'HelixFold3' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (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 | 70% 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 sourceHelixFold3 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 'HelixFold3' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (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 | 3.45% 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 sourceHelixFold3 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 'HelixFold3' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (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 | 23.3% 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 sourceHelixFold3 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 'HelixFold3' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (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 | 0.417 GDT ts 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 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 'HF3', column 'GDT-TS' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (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 | 0.663 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 sourceHelixFold3 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 'HF3', column 'INF' |
| Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (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 | 0.478 lDDT 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 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 'HF3', column 'lDDT' |
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Sources and history
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-hf3-ludaic2026
- areas
- rna-transcriptomes; protein-structure
- contexts
- research
- method types
- foundation_model
- reported name
- HF3
- version
- HelixFold3/73cd80b-hpc1
- 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 'HelixFold3'; Methods 'Model generation'
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