NuFold commit 169a618 (Ludaic and Elofsson 2026 RNA benchmark run)
NuFold 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
16 evaluations · 16 results. Different protocols are not a single leaderboard.
Sorted by GDT ts (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 16 result rows with coverage, uncertainty and sources
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Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: NuFold commit 169a618 (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 | 0.61 GDT ts unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNuFold 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 'NuFold', column 'GDT-TS' |
| Configuration: NuFold commit 169a618 (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 | 0.745 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 sourceNuFold 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 'NuFold', column 'INF' |
| Configuration: NuFold commit 169a618 (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 | 0.599 lDDT unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNuFold 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 'NuFold', column 'lDDT' |
| Configuration: NuFold commit 169a618 (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 | 0.482 TM score unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNuFold 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 'NuFold', column 'TM-score' |
| Configuration: NuFold commit 169a618 (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 | 66.7% 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 sourceNuFold 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 'NuFold' |
| Configuration: NuFold commit 169a618 (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 | 63.3% 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 sourceNuFold 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 'NuFold' |
| Configuration: NuFold commit 169a618 (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 | 20.7% 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 sourceNuFold 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 'NuFold' |
| Configuration: NuFold commit 169a618 (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 | 50% 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 sourceNuFold 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 'NuFold' |
| Configuration: NuFold commit 169a618 (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 sourceNuFold 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 'NuFold', column 'GDT-TS' |
| Configuration: NuFold commit 169a618 (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 | 0.628 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 sourceNuFold 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 'NuFold', column 'INF' |
| Configuration: NuFold commit 169a618 (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 | 0.456 lDDT unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNuFold 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 'NuFold', column 'lDDT' |
| Configuration: NuFold commit 169a618 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA hard set, mean TM-score Dataset: Ludaic and Elofsson 2026 Monomeric RNA hard set | 0.236 TM score unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNuFold on Monomeric RNA hard set (TM-score) lit-rna-20261011-rna3d-protocol-monomer-hard-mean-tm-score Aggregation: Not reported Limits of deep-learning-based RNA prediction methods · Table 3, row 'NuFold', column 'TM-score' |
| Configuration: NuFold commit 169a618 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA hard set, GDT-TS success rate Dataset: Ludaic and Elofsson 2026 Monomeric RNA hard set | 40.8% 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 sourceNuFold on Monomeric RNA hard set (GDT-TS, success rate) lit-rna-20261011-rna3d-protocol-monomer-hard-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 S7, row 'GDT-TS', column 'NuFold' |
| Configuration: NuFold commit 169a618 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA hard set, INF success rate Dataset: Ludaic and Elofsson 2026 Monomeric RNA hard set | 32.6% 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 sourceNuFold on Monomeric RNA hard set (INF, success rate) lit-rna-20261011-rna3d-protocol-monomer-hard-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 S7, row 'INF', column 'NuFold' |
| Configuration: NuFold commit 169a618 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA hard set, lDDT success rate Dataset: Ludaic and Elofsson 2026 Monomeric RNA hard set | 0% 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 sourceNuFold on Monomeric RNA hard set (lDDT, success rate) lit-rna-20261011-rna3d-protocol-monomer-hard-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 S7, row 'lDDT', column 'NuFold' |
| Configuration: NuFold commit 169a618 (Ludaic and Elofsson 2026 RNA benchmark run) | Protocol: Ludaic and Elofsson 2026 Monomeric RNA hard set, TM-score success rate Dataset: Ludaic and Elofsson 2026 Monomeric RNA hard set | 2.04% 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 sourceNuFold on Monomeric RNA hard set (TM-score, success rate) lit-rna-20261011-rna3d-protocol-monomer-hard-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 S7, row 'TM-score', column 'NuFold' |
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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-nufold-ludaic2026
- areas
- rna-transcriptomes; protein-structure
- contexts
- research
- method types
- specialist
- reported name
- NuFold
- version
- commit 169a618
- 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
- false
- source locator
- Supplementary Table S1 row 'NuFold'; Methods 'Model generation'
Related records
- configuration of: NuFold
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- system: NuFold on Monomeric RNA easy set (TM-score)
- system: NuFold on Monomeric RNA easy set (GDT-TS, success rate)
- system: NuFold on Monomeric RNA easy set (INF, success rate)
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- system: NuFold on Monomeric RNA hard set (lDDT)
- system: NuFold on Monomeric RNA hard set (TM-score)
- system: NuFold on Monomeric RNA hard set (GDT-TS, success rate)
- system: NuFold on Monomeric RNA hard set (INF, success rate)
- system: NuFold on Monomeric RNA hard set (lDDT, success rate)
- system: NuFold on Monomeric RNA hard set (TM-score, success rate)