Model type
RNA structure predictor with language-model and MSA inputs
Configuration
RhoFold+
RhoFold+ predicts RNA three-dimensional structures from RNA sequence with alignment information.
Sources (3)
ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadataHow it worksRhoFold+ workflow
Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.
Sources (3)
ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadataOverview
Inputs
RNA FASTA (A, U, G, C), optionally a supplied MSA; an MSA is otherwise generated by the full workflow.
Sources (3)
ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadataOutputs
Three-dimensional PDB models, predicted distograms, secondary structure and per-residue confidence.
Sources (3)
ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadataAccess
Official project documentation and implementation: https://github.com/ml4bio/RhoFold
Sources (3)
ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadatalimited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
6 evaluations · 12 metric rows. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: RhoFold+ | Protocol: RhoFold+ 2024 CASP15 natural RNA comparison R1107-rmsd: R1107: RMSD Dataset subset: CASP15 natural RNA target R1107 (RhoFold+ 2024 CASP15 natural RNA comparison split) | 5.01 Å rmsd angstrom · lower Uncertainty: Not reported Coverage: unit: CASP15 natural RNA target; scored: 1; eligible: 1; note: Per-cell target count; source retains up to five candidate structures, not five independent evaluation targets. | Author-reported evaluation · source checkedMethods, coverage and sourceRhoFold+ on RhoFold+ 2024 CASP15 natural RNA comparison R1107-rmsd: R1107: RMSD Retrospective evaluation of six CASP15 natural single-chain RNA targets; each task retains one named target. Artificially designed targets and RNA-protein complexes excluded. RNA sequence inputs without ions or other molecules. Paper Par13 selects the highest-performing of five candidates; Par51 describes five sampled-MSA runs for RhoFold+, one AlphaFold3 server run yielding five models, and five CASP15 models for the other methods. Figure 2h reports RMSD and sum of Z-scores for GDT-TS and TM-score. Metric-specific winning candidate identity, exact scoring-tool revision and RMSD atom selection remain unextracted. No target pooling or score recomputation. Aggregation: Source-reported selected candidate for one target; no cross-target aggregation. RhoFold+ Nature Methods 2024: Source Data Figure 2h · fig2hi!B11; method fig2hi!A11; target fig2hi!B1; Fig. 2h caption; XML Par13–15 and Par51 |
| Configuration: RhoFold+ | Protocol: RhoFold+ 2024 CASP15 natural RNA comparison R1107-sum_z_gdt_ts_tm_score: R1107: Sum of Z-scores for GDT-TS and TM-score Dataset subset: CASP15 natural RNA target R1107 (RhoFold+ 2024 CASP15 natural RNA comparison split) | 4.68 sum_z_gdt_ts_tm_score dimensionless · higher Uncertainty: Not reported Coverage: unit: CASP15 natural RNA target; scored: 1; eligible: 1; note: Per-cell target count; source retains up to five candidate structures, not five independent evaluation targets. | Author-reported evaluation · source checkedMethods, coverage and sourceRetrospective evaluation of six CASP15 natural single-chain RNA targets; each task retains one named target. Artificially designed targets and RNA-protein complexes excluded. RNA sequence inputs without ions or other molecules. Paper Par13 selects the highest-performing of five candidates; Par51 describes five sampled-MSA runs for RhoFold+, one AlphaFold3 server run yielding five models, and five CASP15 models for the other methods. Figure 2h reports RMSD and sum of Z-scores for GDT-TS and TM-score. Metric-specific winning candidate identity, exact scoring-tool revision and RMSD atom selection remain unextracted. No target pooling or score recomputation. Aggregation: Source-reported selected candidate for one target; no cross-target aggregation. RhoFold+ Nature Methods 2024: Source Data Figure 2h · fig2hi!H11; method fig2hi!A11; target fig2hi!H1; Fig. 2h caption; XML Par13–15 and Par51 |
| Configuration: RhoFold+ | Protocol: RhoFold+ 2024 CASP15 natural RNA comparison R1108-rmsd: R1108: RMSD Dataset subset: CASP15 natural RNA target R1108 (RhoFold+ 2024 CASP15 natural RNA comparison split) | 4.54 Å rmsd angstrom · lower Uncertainty: Not reported Coverage: unit: CASP15 natural RNA target; scored: 1; eligible: 1; note: Per-cell target count; source retains up to five candidate structures, not five independent evaluation targets. | Author-reported evaluation · source checkedMethods, coverage and sourceRhoFold+ on RhoFold+ 2024 CASP15 natural RNA comparison R1108-rmsd: R1108: RMSD Retrospective evaluation of six CASP15 natural single-chain RNA targets; each task retains one named target. Artificially designed targets and RNA-protein complexes excluded. RNA sequence inputs without ions or other molecules. Paper Par13 selects the highest-performing of five candidates; Par51 describes five sampled-MSA runs for RhoFold+, one AlphaFold3 server run yielding five models, and five CASP15 models for the other methods. Figure 2h reports RMSD and sum of Z-scores for GDT-TS and TM-score. Metric-specific winning candidate identity, exact scoring-tool revision and RMSD atom selection remain unextracted. No target pooling or score recomputation. Aggregation: Source-reported selected candidate for one target; no cross-target aggregation. RhoFold+ Nature Methods 2024: Source Data Figure 2h · fig2hi!C11; method fig2hi!A11; target fig2hi!C1; Fig. 2h caption; XML Par13–15 and Par51 |
| Configuration: RhoFold+ | Protocol: RhoFold+ 2024 CASP15 natural RNA comparison R1108-sum_z_gdt_ts_tm_score: R1108: Sum of Z-scores for GDT-TS and TM-score Dataset subset: CASP15 natural RNA target R1108 (RhoFold+ 2024 CASP15 natural RNA comparison split) | 4.5199999999999996 sum_z_gdt_ts_tm_score dimensionless · higher Uncertainty: Not reported Coverage: unit: CASP15 natural RNA target; scored: 1; eligible: 1; note: Per-cell target count; source retains up to five candidate structures, not five independent evaluation targets. | Author-reported evaluation · source checkedMethods, coverage and sourceRetrospective evaluation of six CASP15 natural single-chain RNA targets; each task retains one named target. Artificially designed targets and RNA-protein complexes excluded. RNA sequence inputs without ions or other molecules. Paper Par13 selects the highest-performing of five candidates; Par51 describes five sampled-MSA runs for RhoFold+, one AlphaFold3 server run yielding five models, and five CASP15 models for the other methods. Figure 2h reports RMSD and sum of Z-scores for GDT-TS and TM-score. Metric-specific winning candidate identity, exact scoring-tool revision and RMSD atom selection remain unextracted. No target pooling or score recomputation. Aggregation: Source-reported selected candidate for one target; no cross-target aggregation. RhoFold+ Nature Methods 2024: Source Data Figure 2h · fig2hi!I11; method fig2hi!A11; target fig2hi!I1; Fig. 2h caption; XML Par13–15 and Par51 |
| Configuration: RhoFold+ | Protocol: RhoFold+ 2024 CASP15 natural RNA comparison R1116-rmsd: R1116: RMSD Dataset subset: CASP15 natural RNA target R1116 (RhoFold+ 2024 CASP15 natural RNA comparison split) | 8.92 Å rmsd angstrom · lower Uncertainty: Not reported Coverage: unit: CASP15 natural RNA target; scored: 1; eligible: 1; note: Per-cell target count; source retains up to five candidate structures, not five independent evaluation targets. | Author-reported evaluation · source checkedMethods, coverage and sourceRhoFold+ on RhoFold+ 2024 CASP15 natural RNA comparison R1116-rmsd: R1116: RMSD Retrospective evaluation of six CASP15 natural single-chain RNA targets; each task retains one named target. Artificially designed targets and RNA-protein complexes excluded. RNA sequence inputs without ions or other molecules. Paper Par13 selects the highest-performing of five candidates; Par51 describes five sampled-MSA runs for RhoFold+, one AlphaFold3 server run yielding five models, and five CASP15 models for the other methods. Figure 2h reports RMSD and sum of Z-scores for GDT-TS and TM-score. Metric-specific winning candidate identity, exact scoring-tool revision and RMSD atom selection remain unextracted. No target pooling or score recomputation. Aggregation: Source-reported selected candidate for one target; no cross-target aggregation. RhoFold+ Nature Methods 2024: Source Data Figure 2h · fig2hi!D11; method fig2hi!A11; target fig2hi!D1; Fig. 2h caption; XML Par13–15 and Par51 |
| Configuration: RhoFold+ | Protocol: RhoFold+ 2024 CASP15 natural RNA comparison R1116-sum_z_gdt_ts_tm_score: R1116: Sum of Z-scores for GDT-TS and TM-score Dataset subset: CASP15 natural RNA target R1116 (RhoFold+ 2024 CASP15 natural RNA comparison split) | 2.68 sum_z_gdt_ts_tm_score dimensionless · higher Uncertainty: Not reported Coverage: unit: CASP15 natural RNA target; scored: 1; eligible: 1; note: Per-cell target count; source retains up to five candidate structures, not five independent evaluation targets. | Author-reported evaluation · source checkedMethods, coverage and sourceRetrospective evaluation of six CASP15 natural single-chain RNA targets; each task retains one named target. Artificially designed targets and RNA-protein complexes excluded. RNA sequence inputs without ions or other molecules. Paper Par13 selects the highest-performing of five candidates; Par51 describes five sampled-MSA runs for RhoFold+, one AlphaFold3 server run yielding five models, and five CASP15 models for the other methods. Figure 2h reports RMSD and sum of Z-scores for GDT-TS and TM-score. Metric-specific winning candidate identity, exact scoring-tool revision and RMSD atom selection remain unextracted. No target pooling or score recomputation. Aggregation: Source-reported selected candidate for one target; no cross-target aggregation. RhoFold+ Nature Methods 2024: Source Data Figure 2h · fig2hi!J11; method fig2hi!A11; target fig2hi!J1; Fig. 2h caption; XML Par13–15 and Par51 |
| Configuration: RhoFold+ | Protocol: RhoFold+ 2024 CASP15 natural RNA comparison R1117-rmsd: R1117: RMSD Dataset subset: CASP15 natural RNA target R1117 (RhoFold+ 2024 CASP15 natural RNA comparison split) | 2.87 Å rmsd angstrom · lower Uncertainty: Not reported Coverage: unit: CASP15 natural RNA target; scored: 1; eligible: 1; note: Per-cell target count; source retains up to five candidate structures, not five independent evaluation targets. | Author-reported evaluation · source checkedMethods, coverage and sourceRhoFold+ on RhoFold+ 2024 CASP15 natural RNA comparison R1117-rmsd: R1117: RMSD Retrospective evaluation of six CASP15 natural single-chain RNA targets; each task retains one named target. Artificially designed targets and RNA-protein complexes excluded. RNA sequence inputs without ions or other molecules. Paper Par13 selects the highest-performing of five candidates; Par51 describes five sampled-MSA runs for RhoFold+, one AlphaFold3 server run yielding five models, and five CASP15 models for the other methods. Figure 2h reports RMSD and sum of Z-scores for GDT-TS and TM-score. Metric-specific winning candidate identity, exact scoring-tool revision and RMSD atom selection remain unextracted. No target pooling or score recomputation. Aggregation: Source-reported selected candidate for one target; no cross-target aggregation. RhoFold+ Nature Methods 2024: Source Data Figure 2h · fig2hi!E11; method fig2hi!A11; target fig2hi!E1; Fig. 2h caption; XML Par13–15 and Par51 |
| Configuration: RhoFold+ | Protocol: RhoFold+ 2024 CASP15 natural RNA comparison R1117-sum_z_gdt_ts_tm_score: R1117: Sum of Z-scores for GDT-TS and TM-score Dataset subset: CASP15 natural RNA target R1117 (RhoFold+ 2024 CASP15 natural RNA comparison split) | 2.0099999999999998 sum_z_gdt_ts_tm_score dimensionless · higher Uncertainty: Not reported Coverage: unit: CASP15 natural RNA target; scored: 1; eligible: 1; note: Per-cell target count; source retains up to five candidate structures, not five independent evaluation targets. | Author-reported evaluation · source checkedMethods, coverage and sourceRetrospective evaluation of six CASP15 natural single-chain RNA targets; each task retains one named target. Artificially designed targets and RNA-protein complexes excluded. RNA sequence inputs without ions or other molecules. Paper Par13 selects the highest-performing of five candidates; Par51 describes five sampled-MSA runs for RhoFold+, one AlphaFold3 server run yielding five models, and five CASP15 models for the other methods. Figure 2h reports RMSD and sum of Z-scores for GDT-TS and TM-score. Metric-specific winning candidate identity, exact scoring-tool revision and RMSD atom selection remain unextracted. No target pooling or score recomputation. Aggregation: Source-reported selected candidate for one target; no cross-target aggregation. RhoFold+ Nature Methods 2024: Source Data Figure 2h · fig2hi!K11; method fig2hi!A11; target fig2hi!K1; Fig. 2h caption; XML Par13–15 and Par51 |
| Configuration: RhoFold+ | Protocol: RhoFold+ 2024 CASP15 natural RNA comparison R1149-rmsd: R1149: RMSD Dataset subset: CASP15 natural RNA target R1149 (RhoFold+ 2024 CASP15 natural RNA comparison split) | 7.66 Å rmsd angstrom · lower Uncertainty: Not reported Coverage: unit: CASP15 natural RNA target; scored: 1; eligible: 1; note: Per-cell target count; source retains up to five candidate structures, not five independent evaluation targets. | Author-reported evaluation · source checkedMethods, coverage and sourceRhoFold+ on RhoFold+ 2024 CASP15 natural RNA comparison R1149-rmsd: R1149: RMSD Retrospective evaluation of six CASP15 natural single-chain RNA targets; each task retains one named target. Artificially designed targets and RNA-protein complexes excluded. RNA sequence inputs without ions or other molecules. Paper Par13 selects the highest-performing of five candidates; Par51 describes five sampled-MSA runs for RhoFold+, one AlphaFold3 server run yielding five models, and five CASP15 models for the other methods. Figure 2h reports RMSD and sum of Z-scores for GDT-TS and TM-score. Metric-specific winning candidate identity, exact scoring-tool revision and RMSD atom selection remain unextracted. No target pooling or score recomputation. Aggregation: Source-reported selected candidate for one target; no cross-target aggregation. RhoFold+ Nature Methods 2024: Source Data Figure 2h · fig2hi!F11; method fig2hi!A11; target fig2hi!F1; Fig. 2h caption; XML Par13–15 and Par51 |
| Configuration: RhoFold+ | Protocol: RhoFold+ 2024 CASP15 natural RNA comparison R1149-sum_z_gdt_ts_tm_score: R1149: Sum of Z-scores for GDT-TS and TM-score Dataset subset: CASP15 natural RNA target R1149 (RhoFold+ 2024 CASP15 natural RNA comparison split) | 3.75 sum_z_gdt_ts_tm_score dimensionless · higher Uncertainty: Not reported Coverage: unit: CASP15 natural RNA target; scored: 1; eligible: 1; note: Per-cell target count; source retains up to five candidate structures, not five independent evaluation targets. | Author-reported evaluation · source checkedMethods, coverage and sourceRetrospective evaluation of six CASP15 natural single-chain RNA targets; each task retains one named target. Artificially designed targets and RNA-protein complexes excluded. RNA sequence inputs without ions or other molecules. Paper Par13 selects the highest-performing of five candidates; Par51 describes five sampled-MSA runs for RhoFold+, one AlphaFold3 server run yielding five models, and five CASP15 models for the other methods. Figure 2h reports RMSD and sum of Z-scores for GDT-TS and TM-score. Metric-specific winning candidate identity, exact scoring-tool revision and RMSD atom selection remain unextracted. No target pooling or score recomputation. Aggregation: Source-reported selected candidate for one target; no cross-target aggregation. RhoFold+ Nature Methods 2024: Source Data Figure 2h · fig2hi!L11; method fig2hi!A11; target fig2hi!L1; Fig. 2h caption; XML Par13–15 and Par51 |
| Configuration: RhoFold+ | Protocol: RhoFold+ 2024 CASP15 natural RNA comparison R1156-rmsd: R1156: RMSD Dataset subset: CASP15 natural RNA target R1156 (RhoFold+ 2024 CASP15 natural RNA comparison split) | 17.43 Å rmsd angstrom · lower Uncertainty: Not reported Coverage: unit: CASP15 natural RNA target; scored: 1; eligible: 1; note: Per-cell target count; source retains up to five candidate structures, not five independent evaluation targets. | Author-reported evaluation · source checkedMethods, coverage and sourceRhoFold+ on RhoFold+ 2024 CASP15 natural RNA comparison R1156-rmsd: R1156: RMSD Retrospective evaluation of six CASP15 natural single-chain RNA targets; each task retains one named target. Artificially designed targets and RNA-protein complexes excluded. RNA sequence inputs without ions or other molecules. Paper Par13 selects the highest-performing of five candidates; Par51 describes five sampled-MSA runs for RhoFold+, one AlphaFold3 server run yielding five models, and five CASP15 models for the other methods. Figure 2h reports RMSD and sum of Z-scores for GDT-TS and TM-score. Metric-specific winning candidate identity, exact scoring-tool revision and RMSD atom selection remain unextracted. No target pooling or score recomputation. Aggregation: Source-reported selected candidate for one target; no cross-target aggregation. RhoFold+ Nature Methods 2024: Source Data Figure 2h · fig2hi!G11; method fig2hi!A11; target fig2hi!G1; Fig. 2h caption; XML Par13–15 and Par51 |
| Configuration: RhoFold+ | Protocol: RhoFold+ 2024 CASP15 natural RNA comparison R1156-sum_z_gdt_ts_tm_score: R1156: Sum of Z-scores for GDT-TS and TM-score Dataset subset: CASP15 natural RNA target R1156 (RhoFold+ 2024 CASP15 natural RNA comparison split) | 1.32 sum_z_gdt_ts_tm_score dimensionless · higher Uncertainty: Not reported Coverage: unit: CASP15 natural RNA target; scored: 1; eligible: 1; note: Per-cell target count; source retains up to five candidate structures, not five independent evaluation targets. | Author-reported evaluation · source checkedMethods, coverage and sourceRetrospective evaluation of six CASP15 natural single-chain RNA targets; each task retains one named target. Artificially designed targets and RNA-protein complexes excluded. RNA sequence inputs without ions or other molecules. Paper Par13 selects the highest-performing of five candidates; Par51 describes five sampled-MSA runs for RhoFold+, one AlphaFold3 server run yielding five models, and five CASP15 models for the other methods. Figure 2h reports RMSD and sum of Z-scores for GDT-TS and TM-score. Metric-specific winning candidate identity, exact scoring-tool revision and RMSD atom selection remain unextracted. No target pooling or score recomputation. Aggregation: Source-reported selected candidate for one target; no cross-target aggregation. RhoFold+ Nature Methods 2024: Source Data Figure 2h · fig2hi!M11; method fig2hi!A11; target fig2hi!M1; Fig. 2h caption; XML Par13–15 and Par51 |
Source checking is not independent reproduction. Release 2026-09-23-2b89723c6dd9.
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Related profile: RhoFold+. This page retains the exact record and its evaluation context.
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RhoFold+ automated five-candidate sampled-MSA configuration evaluated by its authors.
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How it works
How it works
RhoFold+ predicts RNA three-dimensional structures from RNA sequence with alignment information. RNA-FM embeddings and MSA representations enter the Rhoformer transformer stack; a geometry-aware invariant-point-attention structure module predicts frames and torsion angles with recycling. The documented inputs are RNA FASTA (A, U, G, C), optionally a supplied MSA; an MSA is otherwise generated by the full workflow. The output consists of three-dimensional PDB models, predicted distograms, secondary structure and per-residue confidence.
Sources (3)
ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadataVersions and reproducibility
RhoFold+; the README links a pretrained checkpoint and the 2024 Nature Methods paper. The paper limits MSA depth to256 sequences during training and default inference. This is alignment depth, not an RNA-length maximum; the latter remains unextracted.
Sources (3)
ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadataStrengths, limitations and unresolved questions
Strengths and limitations
Strengths and considerations
- Produces secondary and tertiary outputs and supports provided or automatically generated alignments.
Sources (3)
ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadata
Limitations and conditions
- The README labels sequence-only inference as a lower-accuracy testing mode. Constructing the full MSA databases needs substantial local storage; macOS is not supported by its documented setup.
Sources (3)
ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadata
Profile review details
Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied.
Stable record: catalog-model-rhofoldSpecifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Model type | RNA structure predictor with language-model and MSA inputsSources (3)ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadata |
| Architecture | RNA-FM embeddings and MSA representations enter the Rhoformer transformer stack; a geometry-aware invariant-point-attention structure module predicts frames and torsion angles with recycling.Sources (3)ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadata |
| Inputs | RNA FASTA (A, U, G, C), optionally a supplied MSA; an MSA is otherwise generated by the full workflow.Sources (3)ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadata |
| Outputs | Three-dimensional PDB models, predicted distograms, secondary structure and per-residue confidence.Sources (3)ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadata |
| Parameters | The inspected paper describes RNA-FM, Rhoformer and structure modules without stating a total for the complete selected predictor in those architecture sections. · Not reported in inspected sourcesSources (3)ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadata |
| Known versions | RhoFold+; the README links a pretrained checkpoint and the 2024 Nature Methods paper.Sources (3)ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadata |
| Training data | RNA-FM pretraining uses RNAcentral100. Structure training uses PDB RNA chains selected through BGSU representative sets, with additional self-distillation from RNAStralign/bpRNA-derived sequences.Sources (3)ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadata |
| Training cutoff | Structural-data selection uses the BGSU representative set dated 2022-04-13. This does not establish a single cutoff for every RNA-FM or MSA resource.Sources (3)ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadata |
| Context limits | MSA depth is capped at 256 during documented training and default inference. The reviewed paper does not establish a single RNA-length maximum; MSA depth is a different quantity. · Not reported in inspected sourcesSources (3)ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadata |
| Weights licence | Apache-2.0 declared in the official cuhkaih/rhofold model-card metadata; this is distinct from access conditions for training data.Sources (3)ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadata |
| Access | Official project documentation and implementation: https://github.com/ml4bio/RhoFoldSources (3)ml4bio/RhoFold: README.md; cuhkaih/rhofold: README.md; rhofold: Journal full-text XML · Paper: Automated end-to-end platform, Large-scale pretraining dataset, Efficient development of a self-distillation dataset, Feature processing with Rhoformer and Data availability; README.md: Usage; official cuhkaih/rhofold card licence metadata |
| Code licence | Apache-2.0Sourcesml4bio/RhoFold: LICENSE · LICENSE: licence text |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: family catalog-model-rhofold Individual claims | RhoFold+ Nature Methods 2024: Source Data Figure 2h fig2hi!A11; Figure 2h; primary XML Par13–15 and Par51 Version: Publisher Source Data Fig. 2, DOI 10.1038/s41592-024-02487-0; retrieved 2026-09-23 | source checked automated source review · 2026-09-23 Audit detailsSource-backed evaluated identity only; no independent reproduction. Field: Claim: rhofold-2024-casp15-natural-method-rhofold-plus-catalog-model-rhofold-identity-claim Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
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Release 2026-09-23-2b89723c6dd9 · Record review: source checked
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- RhoFold+ Nature Methods 2024: Source Data Figure 2h · Original source · Publisher Source Data Fig. 2, DOI 10.1038/s41592-024-02487-0; retrieved 2026-09-23
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Stable ID: rhofold-2024-casp15-natural-method-rhofold-plus
- areas
- rna-transcriptomics
- source locator
- fig2hi!A11; Figure 2h; primary XML Par13–15 and Par51
- missing metadata
- checkpoint revision: unreported; parameters: unextracted
Related records
- family: RhoFold+
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- subject: RhoFold+: family catalog-model-rhofold