Model type
Graph-based predictive method; this record is the paper-specific evaluated configuration.
Configuration
R3Design
R3Design generates RNA sequences conditioned on a tertiary backbone.
Sources
R3Design: deep tertiary structure-based RNA sequence design and beyond · Methods/The R3Design framework (paragraph 4); Methods/The R3Design framework (paragraph 1)How it worksEvaluated procedure (conceptual)
Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings.
Sources
R3Design: deep tertiary structure-based RNA sequence design and beyond · Methods/The R3Design framework (paragraph 4); Methods/The R3Design framework (paragraph 2)At a glance
Biological inputs
RNA tertiary-structure backbone graphs
Sources
R3Design: deep tertiary structure-based RNA sequence design and beyond · Methods/The R3Design framework (paragraph 1); Methods/The R3Design framework (paragraph 5)Outputs
RNA nucleotide sequences designed for the supplied backbone
Sources
R3Design: deep tertiary structure-based RNA sequence design and beyond · Methods/Graph-based RNA tertiary structure modeling (paragraph 9); Methods/Graph-based RNA tertiary structure modeling (paragraph 7)limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
Release 2026-09-17-d277315f7d76 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| R3Design: RNA sequence design Tertiary-structure-conditioned RNA sequence design; external Rfam assessment Author-reported evaluation · Evaluation metadata: needs review | ||
| 43.27% sequence recovery Unit: percent · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedR3Design: deep tertiary structure-based RNA sequence design and beyond · Table 3, R3Design row, Recovery (%) > Rfam column Source checking is not independent reproduction. |
How it works
How the evaluated method works
Three PiGNN layers, adapted from PiFold, encode a graph of the RNA backbone and spatial nucleotide relationships before sequence prediction.
Sources
R3Design: deep tertiary structure-based RNA sequence design and beyond · Methods/The R3Design framework (paragraph 4); Methods/The R3Design framework (paragraph 2)What was evaluated
The linked evaluation record identifies R3Design: RNA sequence design. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
R3Design: deep tertiary structure-based RNA sequence design and beyond · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-b4-006Strengths and limitations
Strengths and considerations
- Evaluates native-backbone sequence recovery and checks generated sequences with structure-prediction models.
Sources
R3Design: deep tertiary structure-based RNA sequence design and beyond · Methods/The R3Design framework (paragraph 5); Methods/The R3Design framework (paragraph 1)
Limitations and conditions
- Computational refolding is not experimental validation that a designed RNA adopts the intended structure or function.
Sources
R3Design: deep tertiary structure-based RNA sequence design and beyond · Methods/The R3Design framework (paragraph 5); Results/The designed sequence can fold into desirable tertiary structure (paragraph 1)
Profile review details
Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction.
Stable record: reported-model-1b5fa066945d3dSpecifications
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 | Graph-based predictive method; this record is the paper-specific evaluated configuration.SourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Methods/The R3Design framework (paragraph 4); Methods/The R3Design framework (paragraph 2) |
| Architecture / procedure | Three PiGNN layers, adapted from PiFold, encode a graph of the RNA backbone and spatial nucleotide relationships before sequence prediction.SourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Methods/The R3Design framework (paragraph 4); Methods/The R3Design framework (paragraph 2) |
| Biological inputs | RNA tertiary-structure backbone graphsSourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Methods/The R3Design framework (paragraph 1); Methods/The R3Design framework (paragraph 5) |
| Outputs | RNA nucleotide sequences designed for the supplied backboneSourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Methods/Graph-based RNA tertiary structure modeling (paragraph 9); Methods/Graph-based RNA tertiary structure modeling (paragraph 7) |
| Parameters | An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)R3Design: deep tertiary structure-based RNA sequence design and beyond; A4Bio/R3Design readme.md · Methods/Preliminaries; Methods/Graph-based RNA tertiary structure modeling; Methods/The R3Design framework; inspected for aggregate parameter count (component sizes are not added without an exact configuration); readme.md at pinned repository revision |
| Known versions / configuration | R3Design is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sourcesSourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. |
| Training data / fitting | 2,218 representative RNA structures from PDB/RNASolo, filtered to resolution below 4Å and at most 500 nucleotides. A structural-similarity split assigns 1,774 training,223 validation and 221 test structures.SourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Results/R3Design designs RNA sequences with high sequence-level fidelity (paragraph 1); Results/The designed sequence can fold into desirable tertiary structure (paragraph 2) |
| Context limits | The curated training/evaluation set excludes RNAs longer than 500 nucleotides; this is a dataset restriction, not a proved inference maximum.SourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Results/R3Design designs RNA sequences with high sequence-level fidelity (paragraph 1); Table TB2 (paragraph 1) |
| Access | Official study implementation and usage documentation: https://github.com/A4Bio/R3Design/blob/c05dc4b35100949011c77c08f61a9e80280987ce/readme.md. This pinned documentation revision is not automatically the evaluated weight revision.SourcesA4Bio/R3Design readme.md · readme.md; installation, model download and usage instructions |
| Code licence | No explicit code licence was established from the paper’s availability statement and inspected repository-root documentation. · Not reported in inspected sourcesSourcesA4Bio/R3Design readme.md · readme.md and repository-root licence-file search |
| Weights licence | The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. · Not reported in inspected sourcesSourcesA4Bio/R3Design readme.md · readme.md; checkpoint/access documentation and licence scope |
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.
20 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings. Individual claims | R3Design: deep tertiary structure-based RNA sequence design and beyond Methods/The R3Design framework (paragraph 4); Methods/The R3Design framework (paragraph 2) Version: PMC archival version PMC11685104.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["RNA tertiary-structure backbone graphs","R3Design","RNA nucleotide sequences designed for the supplied backbone"] Individual claims | R3Design: deep tertiary structure-based RNA sequence design and beyond Methods/The R3Design framework (paragraph 4); Methods/The R3Design framework (paragraph 2) Version: PMC archival version PMC11685104.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Evaluated procedure (conceptual) Individual claims | R3Design: deep tertiary structure-based RNA sequence design and beyond Methods/The R3Design framework (paragraph 4); Methods/The R3Design framework (paragraph 2) Version: PMC archival version PMC11685104.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Model type Graph-based predictive method; this record is the paper-specific evaluated configuration. Individual claims | R3Design: deep tertiary structure-based RNA sequence design and beyond Methods/The R3Design framework (paragraph 4); Methods/The R3Design framework (paragraph 2) Version: PMC archival version PMC11685104.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Architecture / procedure Three PiGNN layers, adapted from PiFold, encode a graph of the RNA backbone and spatial nucleotide relationships before sequence prediction. Individual claims | R3Design: deep tertiary structure-based RNA sequence design and beyond Methods/The R3Design framework (paragraph 4); Methods/The R3Design framework (paragraph 2) Version: PMC archival version PMC11685104.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Weights licence The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. Individual claims | A4Bio/R3Design readme.md readme.md; checkpoint/access documentation and licence scope Version: c05dc4b35100949011c77c08f61a9e80280987ce | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Biological inputs RNA tertiary-structure backbone graphs Individual claims | R3Design: deep tertiary structure-based RNA sequence design and beyond Methods/The R3Design framework (paragraph 1); Methods/The R3Design framework (paragraph 5) Version: PMC archival version PMC11685104.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Outputs RNA nucleotide sequences designed for the supplied backbone Individual claims | R3Design: deep tertiary structure-based RNA sequence design and beyond Methods/Graph-based RNA tertiary structure modeling (paragraph 9); Methods/Graph-based RNA tertiary structure modeling (paragraph 7) Version: PMC archival version PMC11685104.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | A4Bio/R3Design readme.md Methods/Preliminaries; Methods/Graph-based RNA tertiary structure modeling; Methods/The R3Design framework; inspected for aggregate parameter count (component sizes are not added without an exact configuration); readme.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: c05dc4b35100949011c77c08f61a9e80280987ce | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | R3Design: deep tertiary structure-based RNA sequence design and beyond Methods/Preliminaries; Methods/Graph-based RNA tertiary structure modeling; Methods/The R3Design framework; inspected for aggregate parameter count (component sizes are not added without an exact configuration); readme.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC archival version PMC11685104.1 | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
2 source records and release history
- R3Design: deep tertiary structure-based RNA sequence design and beyond · Original source · PMC archival version PMC11685104.1
- A4Bio/R3Design readme.md · Original source · c05dc4b35100949011c77c08f61a9e80280987ce
Technical metadata and extraction receipts
Stable ID: reported-model-1b5fa066945d3d
- areas
- rna-transcriptomes
- entity level
- method
- version
- Not reported
- reported name
- R3Design
- historical missing metadata
- version: not_reported_in_legacy_extract; checkpoint revision: not_reported_in_legacy_extract; training data: not_reported_in_legacy_extract; licence: not_reported_in_legacy_extract
- metadata review scope
- historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
- legacy kinds
- model
- entity classification
- review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: r3design-2025; source locator: Methods/The R3Design framework (paragraph 4); Methods/The R3Design framework (paragraph 2) | Methods/The R3Design framework (paragraph 4); Methods/The R3Design framework (paragraph 1); ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.