Model type
Diffusion-based protein backbone generator
RFdiffusion generates protein structures, optionally conditioned on a motif, target or symmetry constraint.
Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.
Diffusion-based protein backbone generator
Unconditional length specification or structural constraints such as a motif, target and contig map.
Generated protein backbone designs for downstream sequence design and assessment.
Official project documentation and implementation: https://github.com/RosettaCommons/RFdiffusion
limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
20 evaluations · 20 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-100-DIVERSITY-MAX-CLUST: length 100, Diversity Max Clust. Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.32 max-clust score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-100-DIVERSITY-MAX-CLUST: length 100, Diversity Max Clust. Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 100, Diversity Max Clust.↑) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-100-DIVERSITY-PAIRWISE-TM: length 100, Diversity pairwise TM Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.41 ± 0.03 pairwise-tm score · lower Uncertainty: type: standard_deviation; value: 0.03 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-100-DIVERSITY-PAIRWISE-TM: length 100, Diversity pairwise TM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 100, Diversity pairwise TM ↓) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-100-NOVELTY-MAX-TM: length 100, Novelty Max TM Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.76 ± 0.01 max-tm score · lower Uncertainty: type: standard_deviation; value: 0.01 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-100-NOVELTY-MAX-TM: length 100, Novelty Max TM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 100, Novelty Max TM ↓) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-100-QUALITY-SCRMSD: length 100, Quality scRMSD Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.48 ± 0.56 scrmsd score · lower Uncertainty: type: standard_deviation; value: 0.56 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-100-QUALITY-SCRMSD: length 100, Quality scRMSD Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 100, Quality scRMSD ↓) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-100-QUALITY-SCTM: length 100, Quality scTM Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.98 ± 0.12 sctm score · higher Uncertainty: type: standard_deviation; value: 0.12 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-100-QUALITY-SCTM: length 100, Quality scTM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 100, Quality scTM ↑) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-300-DIVERSITY-MAX-CLUST: length 300, Diversity Max Clust. Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.65 max-clust score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-300-DIVERSITY-MAX-CLUST: length 300, Diversity Max Clust. Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 300, Diversity Max Clust. ↑) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-300-DIVERSITY-PAIRWISE-TM: length 300, Diversity pairwise TM Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.36 ± 0.03 pairwise-tm score · lower Uncertainty: type: standard_deviation; value: 0.03 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-300-DIVERSITY-PAIRWISE-TM: length 300, Diversity pairwise TM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 300, Diversity pairwise TM ↓) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-300-NOVELTY-MAX-TM: length 300, Novelty Max TM Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.64 ± 0.01 max-tm score · lower Uncertainty: type: standard_deviation; value: 0.01 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-300-NOVELTY-MAX-TM: length 300, Novelty Max TM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 300, Novelty Max TM ↓) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-300-QUALITY-SCRMSD: length 300, Quality scRMSD Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 1.03 ± 3.14 scrmsd score · lower Uncertainty: type: standard_deviation; value: 3.14 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-300-QUALITY-SCRMSD: length 300, Quality scRMSD Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 300, Quality scRMSD ↓) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-300-QUALITY-SCTM: length 300, Quality scTM Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.96 ± 0.15 sctm score · higher Uncertainty: type: standard_deviation; value: 0.15 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-300-QUALITY-SCTM: length 300, Quality scTM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 300, Quality scTM ↑) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-50-DIVERSITY-MAX-CLUST: length 50, Diversity Max Clust. Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.67 max-clust score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-50-DIVERSITY-MAX-CLUST: length 50, Diversity Max Clust. Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 50, Diversity Max Clust. ↑) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-50-DIVERSITY-PAIRWISE-TM: length 50, Diversity pairwise TM Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.58 ± 0.05 pairwise-tm score · lower Uncertainty: type: standard_deviation; value: 0.05 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-50-DIVERSITY-PAIRWISE-TM: length 50, Diversity pairwise TM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 50, Diversity pairwise TM ↓) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-50-NOVELTY-MAX-TM: length 50, Novelty Max TM Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.65 ± 0.16 max-tm score · lower Uncertainty: type: standard_deviation; value: 0.16 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-50-NOVELTY-MAX-TM: length 50, Novelty Max TM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 50, Novelty Max TM ↓) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-50-QUALITY-SCRMSD: length 50, Quality scRMSD Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.45 ± 1.71 scrmsd score · lower Uncertainty: type: standard_deviation; value: 1.71 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-50-QUALITY-SCRMSD: length 50, Quality scRMSD Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 50, Quality scRMSD ↓) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-50-QUALITY-SCTM: length 50, Quality scTM Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.95 ± 0.12 sctm score · higher Uncertainty: type: standard_deviation; value: 0.12 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-50-QUALITY-SCTM: length 50, Quality scTM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 50, Quality scTM ↑) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-500-DIVERSITY-MAX-CLUST: length 500, Diversity Max Clust. Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.89 max-clust score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-500-DIVERSITY-MAX-CLUST: length 500, Diversity Max Clust. Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 500, Diversity Max Clust.↑) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-500-DIVERSITY-PAIRWISE-TM: length 500, Diversity pairwise TM Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.33 ± 0.02 pairwise-tm score · lower Uncertainty: type: standard_deviation; value: 0.02 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-500-DIVERSITY-PAIRWISE-TM: length 500, Diversity pairwise TM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 500, Diversity pairwise TM ↓) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-500-NOVELTY-MAX-TM: length 500, Novelty Max TM Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.62 ± 0.004 max-tm score · lower Uncertainty: type: standard_deviation; value: 0.004 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-500-NOVELTY-MAX-TM: length 500, Novelty Max TM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 500, Novelty Max TM ↓) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-500-QUALITY-SCRMSD: length 500, Quality scRMSD Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 5.60 ± 5.66 scrmsd score · lower Uncertainty: type: standard_deviation; value: 5.66 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-500-QUALITY-SCRMSD: length 500, Quality scRMSD Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 500, Quality scRMSD ↓) |
| Configuration: RFdiffusion | Task: ProteinBench BB-LENGTH-500-QUALITY-SCTM: length 500, Quality scTM Dataset subset: Designed backbones at fixed lengths (ProteinBench split) | 0.79 ± 0.19 sctm score · higher Uncertainty: type: standard_deviation; value: 0.19 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRFdiffusion on ProteinBench BB-LENGTH-500-QUALITY-SCTM: length 500, Quality scTM Unconditional backbone design at a fixed sequence length. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 3, row(RFdiffusion), column(length 500, Quality scTM ↑) |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Related profile: RFdiffusion. This page retains the exact record and its evaluation context.
Protein model evaluated by the ProteinBench authors under their harness.
RFdiffusion generates protein structures, optionally conditioned on a motif, target or symmetry constraint. Diffusion-based protein structure generation with checkpoint-specific conditioning and denoising configuration. The documented inputs are unconditional length specification or structural constraints such as a motif, target and contig map. The output consists of generated protein backbone designs for downstream sequence design and assessment.
Base, active-site, sequence-inpainting and other conditioning-specific checkpoints; preserve the selected weight identity. The RFdiffusion training crop is 384 residues (supplementary Table 6). This crop size is not an inference maximum; contig lengths and conditional task settings remain explicit.
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: discovery-model-rfdiffusionExplanatory 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 | Diffusion-based protein backbone generatorSources (3)RosettaCommons/RFdiffusion: README.md; rfdiffusion: Journal full-text XML; rfdiffusion-supp: Publisher supplementary archive · RFdiffusion paper Main text and Extended Data Figure 1 (pretrained representations); README.md: model variants, contigs and licence; Supplementary Methods Sections 1.4 and 4.1, Table 6 |
| Architecture | Diffusion-based protein structure generation with checkpoint-specific conditioning and denoising configuration.Sources (3)RosettaCommons/RFdiffusion: README.md; rfdiffusion: Journal full-text XML; rfdiffusion-supp: Publisher supplementary archive · RFdiffusion paper Main text and Extended Data Figure 1 (pretrained representations); README.md: model variants, contigs and licence; Supplementary Methods Sections 1.4 and 4.1, Table 6 |
| Inputs | Unconditional length specification or structural constraints such as a motif, target and contig map.Sources (3)RosettaCommons/RFdiffusion: README.md; rfdiffusion: Journal full-text XML; rfdiffusion-supp: Publisher supplementary archive · RFdiffusion paper Main text and Extended Data Figure 1 (pretrained representations); README.md: model variants, contigs and licence; Supplementary Methods Sections 1.4 and 4.1, Table 6 |
| Outputs | Generated protein backbone designs for downstream sequence design and assessment.Sources (3)RosettaCommons/RFdiffusion: README.md; rfdiffusion: Journal full-text XML; rfdiffusion-supp: Publisher supplementary archive · RFdiffusion paper Main text and Extended Data Figure 1 (pretrained representations); README.md: model variants, contigs and licence; Supplementary Methods Sections 1.4 and 4.1, Table 6 |
| Parameters | The complete supplementary architecture and training sections specify RoseTTAFold-derived modules and training settings but do not state a total for each released conditional checkpoint. · Not reported in inspected sourcesSources (3)RosettaCommons/RFdiffusion: README.md; rfdiffusion: Journal full-text XML; rfdiffusion-supp: Publisher supplementary archive · RFdiffusion paper Main text and Extended Data Figure 1 (pretrained representations); README.md: model variants, contigs and licence; Supplementary Methods Sections 1.4 and 4.1, Table 6 |
| Known versions | Base, active-site, sequence-inpainting and other conditioning-specific checkpoints; preserve the selected weight identity.Sources (3)RosettaCommons/RFdiffusion: README.md; rfdiffusion: Journal full-text XML; rfdiffusion-supp: Publisher supplementary archive · RFdiffusion paper Main text and Extended Data Figure 1 (pretrained representations); README.md: model variants, contigs and licence; Supplementary Methods Sections 1.4 and 4.1, Table 6 |
| Training data | Fine-tunes pretrained RoseTTAFold to denoise protein backbone structures from the PDB; unconditional and task-conditioned variants are distinct configurations.Sources (3)RosettaCommons/RFdiffusion: README.md; rfdiffusion: Journal full-text XML; rfdiffusion-supp: Publisher supplementary archive · RFdiffusion paper Main text and Extended Data Figure 1 (pretrained representations); README.md: model variants, contigs and licence; Supplementary Methods Sections 1.4 and 4.1, Table 6 |
| Training cutoff | The supplementary RoseTTAFold pretraining description specifies a 2 August 2021 PDB cutoff and additional AlphaFold2 models. This is pretraining provenance, not a date for every conditional design fine-tune.Sources (3)RosettaCommons/RFdiffusion: README.md; rfdiffusion: Journal full-text XML; rfdiffusion-supp: Publisher supplementary archive · RFdiffusion paper Main text and Extended Data Figure 1 (pretrained representations); README.md: model variants, contigs and licence; Supplementary Methods Sections 1.4 and 4.1, Table 6 |
| Context limits | The RFdiffusion training crop is 384 residues (supplementary Table 6). This crop size is not an inference maximum; contig lengths and conditional task settings remain explicit.Sources (3)RosettaCommons/RFdiffusion: README.md; rfdiffusion: Journal full-text XML; rfdiffusion-supp: Publisher supplementary archive · RFdiffusion paper Main text and Extended Data Figure 1 (pretrained representations); README.md: model variants, contigs and licence; Supplementary Methods Sections 1.4 and 4.1, Table 6 |
| Weights licence | BSD licence in the inspected LICENSE explicitly covers both source code and linked downloadable model weights.Sources (3)RosettaCommons/RFdiffusion: README.md; rfdiffusion: Journal full-text XML; rfdiffusion-supp: Publisher supplementary archive · RFdiffusion paper Main text and Extended Data Figure 1 (pretrained representations); README.md: model variants, contigs and licence; Supplementary Methods Sections 1.4 and 4.1, Table 6 |
| Access | Official project documentation and implementation: https://github.com/RosettaCommons/RFdiffusionSources (3)RosettaCommons/RFdiffusion: README.md; rfdiffusion: Journal full-text XML; rfdiffusion-supp: Publisher supplementary archive · RFdiffusion paper Main text and Extended Data Figure 1 (pretrained representations); README.md: model variants, contigs and licence; Supplementary Methods Sections 1.4 and 4.1, Table 6 |
| Code licence | BSD-3-ClauseSourcesRosettaCommons/RFdiffusion: LICENSE · LICENSE: licence text |
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| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: family discovery-model-rfdiffusion Individual claims | proteinbench primary benchmark evidence Tables 3; task methods and corresponding named row Version: 2409.06744v1 | source checked automated source review · 2026-09-23 Audit detailsSource review establishes this relationship only. Exact evaluated configurations and original numerical review status remain unchanged. Paper evaluates this named model under its ProteinBench harness. Association is to the family, not an assertion of checkpoint equivalence or cross-task comparability. Field: Claim: model-evaluation-identity-7ab2fb1d706347ec24d1 Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
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Release 2026-09-29-06401fd5b220 · Record review: source checked
Stable ID: proteinbench-method-rfdiffusion