Monomeric RNAs below the 0.5 TM-score similarity cut-off (hard). 49 targets in Supplementary Tables S2-S4; 47 in Table S5 (lDDT).
66 evaluations · 66 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 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' |
| Configuration: AlphaFold3 3.0.1 (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 | 0.245 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 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 'AF3', column 'TM-score' |
| Configuration: AlphaFold3 3.0.1 (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 | 46.9% 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 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 'AF3' |
| Configuration: AlphaFold3 3.0.1 (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 | 6.38% 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 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 'AF3' |
| Configuration: AlphaFold3 3.0.1 (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 | 4.08% 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 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 'AF3' |
| Configuration: Boltz-1 0.4.1 (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 | 0.437 GDT ts 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 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 'Boltz-1', column 'GDT-TS' |
| Configuration: Boltz-1 0.4.1 (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 | 0.673 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 sourceBoltz-1 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 'Boltz-1', column 'INF' |
| Configuration: Boltz-1 0.4.1 (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 | 0.5 lDDT 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 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 'Boltz-1', column 'lDDT' |
| Configuration: Boltz-1 0.4.1 (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 | 0.247 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 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 'Boltz-1', column 'TM-score' |
| Configuration: Boltz-1 0.4.1 (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 | 46.9% 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 sourceBoltz-1 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 'Boltz-1' |
| Configuration: Boltz-1 0.4.1 (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 | 55.1% 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 sourceBoltz-1 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 'Boltz-1' |
| Configuration: Boltz-1 0.4.1 (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 | 10.6% 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 sourceBoltz-1 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 'Boltz-1' |
| Configuration: Boltz-1 0.4.1 (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 | 0% 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 sourceBoltz-1 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 'Boltz-1' |
| Configuration: Chai-1 0.6.1 (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 | 0.406 GDT ts unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceChai-1 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 'Chai-1', column 'GDT-TS' |
| Configuration: Chai-1 0.6.1 (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 | 0.65 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 sourceChai-1 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 'Chai-1', column 'INF' |
| Configuration: Chai-1 0.6.1 (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 | 0.515 lDDT unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceChai-1 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 'Chai-1', column 'lDDT' |
| Configuration: Chai-1 0.6.1 (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 | 0.226 TM score unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceChai-1 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 'Chai-1', column 'TM-score' |
| Configuration: Chai-1 0.6.1 (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 | 38.8% 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 sourceChai-1 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 'Chai-1' |
| Configuration: Chai-1 0.6.1 (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 | 42.9% 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 sourceChai-1 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 'Chai-1' |
| Configuration: Chai-1 0.6.1 (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 | 4.26% 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 sourceChai-1 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 'Chai-1' |
| Configuration: Chai-1 0.6.1 (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 sourceChai-1 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 'Chai-1' |
| Configuration: DeepFoldRNA 1.0 (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 | 0.226 TM score unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDeepFoldRNA 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 'DeepFoldRNA', column 'TM-score' |
| Configuration: DeepFoldRNA 1.0 (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 | 0% 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 sourceDeepFoldRNA 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 'DeepFoldRNA' |
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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 (structurally dissimilar to training data) 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 Monomeric RNAs below the 0.5 TM-score similarity cut-off (hard). 49 targets in Supplementary Tables S2-S4; 47 in Table S5 (lDDT). 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 Monomeric RNA 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-monomer-hard