Configuration

Boltz-1 0.4.1 (Ludaic and Elofsson 2026 RNA benchmark run)

Boltz-1 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

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.

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 (GDT-TS above the CASP16 threshold)	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)
Boltz-1 0.4.1 (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	0.461 (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
Boltz-1 0.4.1 (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	0.446	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
Boltz-1 0.4.1 (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	0.387	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
Boltz-1 0.4.1 (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	0.247	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
Boltz-1 0.4.1 (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	Not reported	0.256	Not reported
Boltz-1 0.4.1 (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	Not reported	0.42
Boltz-1 0.4.1 (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	0.382 (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
Boltz-1 0.4.1 (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	0.346 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Boltz-1 0.4.1 (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	0.808 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Boltz-1 0.4.1 (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	10.2 (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
Boltz-1 0.4.1 (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	24.5 (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
Boltz-1 0.4.1 (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	0.224	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Boltz-1 0.4.1 (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	0.205	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Boltz-1 0.4.1 (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	0.216	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Boltz-1 0.4.1 (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	19.6	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
Boltz-1 0.4.1 (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	41.2	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Boltz-1 0.4.1 (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	0.598 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Boltz-1 0.4.1 (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	0.731 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Boltz-1 0.4.1 (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	0.609 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Boltz-1 0.4.1 (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	73.3% (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported
Boltz-1 0.4.1 (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	Not reported	60% (best in column)	Not reported	Not reported	Not reported	Not reported
Boltz-1 0.4.1 (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	Not reported	13.8% (best in column)	Not reported	Not reported	Not reported
Boltz-1 0.4.1 (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	Not reported	40% (best in column)	Not reported	Not reported
Boltz-1 0.4.1 (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	0.437	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Boltz-1 0.4.1 (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	0.673	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Boltz-1 0.4.1 (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	0.5	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Boltz-1 0.4.1 (Ludaic and Elofsson 2026 RNA benchmark run)Evaluation	Ludaic and Elofsson 2026 Monomeric RNA hard set, GDT-TS 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
Boltz-1 0.4.1 (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	Not reported	55.1%	Not reported	Not reported	Not reported	Not reported
Boltz-1 0.4.1 (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	Not reported	10.6%	Not reported	Not reported	Not reported
Boltz-1 0.4.1 (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	Not reported	0%	Not reported	Not reported

All 30 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Boltz-1 0.4.1 (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	0.256 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 checked Methods, coverage and source Boltz-1 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 'Boltz-1'
Configuration: Boltz-1 0.4.1 (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	0.42 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 checked Methods, coverage and source Boltz-1 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 'Boltz-1'
Configuration: Boltz-1 0.4.1 (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	0.382 DockQ unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz-1 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 'Boltz-1', column 'DockQ'
Configuration: Boltz-1 0.4.1 (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	0.346 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 checked Methods, coverage and source Boltz-1 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 'Boltz-1', column 'F1'
Configuration: Boltz-1 0.4.1 (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	0.808 Fnat unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz-1 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 'Boltz-1', column 'fnat'
Configuration: Boltz-1 0.4.1 (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	10.2 CAPRI interface RMSD angstrom · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz-1 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 'Boltz-1', column 'iRMSD'
Configuration: Boltz-1 0.4.1 (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	24.5 CAPRI ligand RMSD angstrom · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz-1 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 'Boltz-1', column 'LRMSD'
Configuration: Boltz-1 0.4.1 (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	0.387 TM score unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz-1 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 'Boltz-1', column 'TM-score'
Configuration: Boltz-1 0.4.1 (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	0.224 DockQ unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz-1 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 'Boltz-1', column 'DockQ'
Configuration: Boltz-1 0.4.1 (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	0.205 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 checked Methods, coverage and source Boltz-1 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 'Boltz-1', column 'F1'
Configuration: Boltz-1 0.4.1 (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	0.216 Fnat unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz-1 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 'Boltz-1', column 'fnat'
Configuration: Boltz-1 0.4.1 (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	19.6 CAPRI interface RMSD angstrom · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz-1 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 'Boltz-1', column 'iRMSD'
Configuration: Boltz-1 0.4.1 (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	41.2 CAPRI ligand RMSD angstrom · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz-1 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 'Boltz-1', column 'LRMSD'
Configuration: Boltz-1 0.4.1 (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	0.446 TM score unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz-1 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 '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, 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 checked Methods, coverage and source Boltz-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 checked Methods, coverage and source Boltz-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 checked Methods, coverage and source Boltz-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 checked Methods, coverage and source Boltz-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 checked Methods, coverage and source Boltz-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 checked Methods, coverage and source Boltz-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 checked Methods, coverage and source Boltz-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 checked Methods, coverage and source Boltz-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: 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 checked Methods, coverage and source Boltz-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 checked Methods, coverage and source Boltz-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 checked Methods, coverage and source Boltz-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'

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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

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Stable ID: lit-rna-20261011-rna3d-config-boltz-1-ludaic2026

areas: rna-transcriptomes; protein-structure
contexts: research
method types: foundation_model
reported name: Boltz-1
version: 0.4.1
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 'Boltz-1'; Methods 'Model generation'

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