Monomeric RNAs with maximum RNA-align TM-score to the PDB training data at or above the 0.5 cut-off (easy). 30 targets in Supplementary Tables S2-S4; 29 in Table S5 (lDDT).
68 evaluations · 68 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 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: Boltz-1 0.4.1 (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 | 0.598 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 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 '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 easy set, mean INF Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 0.731 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 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 'Boltz-1', column 'INF' |
| Configuration: Boltz-1 0.4.1 (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 | 0.609 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 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 'Boltz-1', column 'lDDT' |
| Configuration: Boltz-1 0.4.1 (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 | 0.461 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 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 '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 easy set, GDT-TS success rate Dataset: Ludaic and Elofsson 2026 Monomeric RNA easy set | 73.3% 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 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 'Boltz-1' |
| Configuration: Boltz-1 0.4.1 (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 | 60% 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 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 'Boltz-1' |
| Configuration: Boltz-1 0.4.1 (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 | 13.8% 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 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 'Boltz-1' |
| Configuration: Boltz-1 0.4.1 (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 | 40% 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 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 'Boltz-1' |
| Configuration: Chai-1 0.6.1 (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 | 0.52 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 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 'Chai', column 'GDT-TS' |
| Configuration: Chai-1 0.6.1 (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 | 0.721 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 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 'Chai', column 'INF' |
| Configuration: Chai-1 0.6.1 (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 | 0.643 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 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 'Chai', column 'lDDT' |
| Configuration: Chai-1 0.6.1 (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 | 0.402 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 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 'Chai', column 'TM-score' |
| Configuration: Chai-1 0.6.1 (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 | 53.3% 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 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 'Chai-1' |
| Configuration: Chai-1 0.6.1 (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 | 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 sourceChai-1 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 'Chai-1' |
| Configuration: Chai-1 0.6.1 (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 | 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 sourceChai-1 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 'Chai-1' |
| Configuration: Chai-1 0.6.1 (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 | 30% 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 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 'Chai-1' |
| Configuration: DeepFoldRNA 1.0 (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 | 0.428 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 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 'DeepFoldRNA', 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 Easy (structurally similar 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 with maximum RNA-align TM-score to the PDB training data at or above the 0.5 cut-off (easy). 30 targets in Supplementary Tables S2-S4; 29 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 easy 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-easy