Datasets
Nonredundant RNA structures from PDB and RNASolo.
Task
RNA sequence design
RNA inverse-folding evaluation uses structure-grouped partitions and computational structure-recovery checks.
Sources
R3Design: deep tertiary structure-based RNA sequence design and beyond · Results: benchmark dataset and structural assessment; cached text lines 10, 31–33Overview
Metrics
Predicted-structure RMSD is among the evaluated outcomes.
Allowed inputs
RNA structural context for sequence prediction.
Sources
R3Design: deep tertiary structure-based RNA sequence design and beyond · Results: benchmark dataset and structural assessment; cached text lines 10, 31–33Evaluation procedure diagram
How it worksComputational evaluation flow
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Sources
R3Design: deep tertiary structure-based RNA sequence design and beyond · Results: benchmark dataset and structural assessment; cached text lines 10, 31–33limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
1 evaluation · 1 result. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: R3Design | Task: RNA sequence design Dataset: Rfam | 43.3% sequence recovery percent · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceTertiary-structure-conditioned RNA sequence design; external Rfam assessment Aggregation: Not reported R3Design: deep tertiary structure-based RNA sequence design and beyond · Table 3, R3Design row, Recovery (%) > Rfam column |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Evaluation methodology
Nonredundant RNA structures from PDB and RNASolo. Training, validation and test allocations are based on structural similarity. Predicted-structure RMSD is among the evaluated outcomes. Structural similarity informs the dataset partition. Three experiments with different seeds report mean and standard deviation.
Sources
R3Design: deep tertiary structure-based RNA sequence design and beyond · Results: benchmark dataset and structural assessment; cached text lines 10, 31–33Recorded evaluations
Each evaluation records what was tested and under which conditions.
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Strengths, limitations and unresolved questions
Strengths and limitations
Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Limitations and conditions
- Structure-predictor agreement is a computational proxy for folding, not experimental validation; predictor dependence remains an evaluation limitation.
Sources
R3Design: deep tertiary structure-based RNA sequence design and beyond · Results: benchmark dataset and structural assessment; cached text lines 10, 31–33
Profile review details
Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged.
Stable record: reported-task-df18c710f45213Specifications
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 |
|---|---|
| Datasets | Nonredundant RNA structures from PDB and RNASolo.SourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 |
| Splits | Training, validation and test allocations are based on structural similarity.SourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 |
| Metrics | Predicted-structure RMSD is among the evaluated outcomes.SourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 |
| Baselines | The core structural benchmark compares SeqRNN and SeqLSTM at two hidden sizes, StructMLP, StructGNN, GraphTrans and PiFold. Separate Rfam/RNA-Puzzles tables include secondary-structure-oriented methods; their scores should retain their own dataset and metric context.SourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Tables 1–3: method-column entries; computational evaluation results |
| Leakage controls | Structural similarity informs the dataset partition.SourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 |
| Uncertainty | Three experiments with different seeds report mean and standard deviation.SourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 |
| Entity type | Paper-specific computational evaluation protocol.SourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 |
| Organisms | RNA structures are selected from PDB/RNASolo, with separate Rfam and RNA-Puzzles evaluations. The curation description reports RNA structural diversity rather than organism membership or species-stratified scores. · Not reported in inspected sourcesSourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Results: benchmark-data curation; Tables 1–3; Data availability |
| Assays | Structural reference backbones and associated RNA sequences.SourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 |
| Allowed inputs | RNA structural context for sequence prediction.SourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 |
| Adaptation | Task training on structurally partitioned data; evaluated with recovery/perplexity and structural consistency criteria.SourcesR3Design: deep tertiary structure-based RNA sequence design and beyond · Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Papers and result coverage
Last literature check: 2026-09-17. Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
| Paper or primary resource | Version | Reference |
|---|---|---|
| R3Design: deep tertiary structure-based RNA sequence design and beyond | PMC archival version PMC11685104.1 | Read source |
Historical gaps recorded on 2026-09-17
The catalogue now holds 1 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.
- complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.
- exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Search and extraction details
primary comparison tables located
Searches
- R3Design: deep tertiary structure-based RNA sequence design and beyond 10.1093/bib/bbae682
Evidence locations
- Table 1; XML table TB1
- Table 2; XML table TB2
- Table 3; XML table TB3
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.
17 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims | R3Design: deep tertiary structure-based RNA sequence design and beyond Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 Version: PMC archival version PMC11685104.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Diagram steps
| R3Design: deep tertiary structure-based RNA sequence design and beyond Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 Version: PMC archival version PMC11685104.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | R3Design: deep tertiary structure-based RNA sequence design and beyond Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 Version: PMC archival version PMC11685104.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets Nonredundant RNA structures from PDB and RNASolo. Individual claims | R3Design: deep tertiary structure-based RNA sequence design and beyond Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 Version: PMC archival version PMC11685104.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits Training, validation and test allocations are based on structural similarity. Individual claims | R3Design: deep tertiary structure-based RNA sequence design and beyond Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 Version: PMC archival version PMC11685104.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Task training on structurally partitioned data; evaluated with recovery/perplexity and structural consistency criteria. Individual claims | R3Design: deep tertiary structure-based RNA sequence design and beyond Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 Version: PMC archival version PMC11685104.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics Predicted-structure RMSD is among the evaluated outcomes. Individual claims | R3Design: deep tertiary structure-based RNA sequence design and beyond Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 Version: PMC archival version PMC11685104.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines The core structural benchmark compares SeqRNN and SeqLSTM at two hidden sizes, StructMLP, StructGNN, GraphTrans and PiFold. Separate Rfam/RNA-Puzzles tables include secondary-structure-oriented methods; their scores should retain their own dataset and metric context. Individual claims | R3Design: deep tertiary structure-based RNA sequence design and beyond Tables 1–3: method-column entries; computational evaluation results Version: PMC archival version PMC11685104.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls Structural similarity informs the dataset partition. Individual claims | R3Design: deep tertiary structure-based RNA sequence design and beyond Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 Version: PMC archival version PMC11685104.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Uncertainty Three experiments with different seeds report mean and standard deviation. Individual claims | R3Design: deep tertiary structure-based RNA sequence design and beyond Results: benchmark dataset and structural assessment; cached text lines 10, 31–33 Version: PMC archival version PMC11685104.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · 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
- R3Design: deep tertiary structure-based RNA sequence design and beyond · Original source · PMC archival version PMC11685104.1
Technical metadata and extraction receipts
Stable ID: reported-task-df18c710f45213
- areas
- rna-transcriptomes
- tasks
- RNA sequence design
- entity level
- task
- version
- Not reported
- task
- RNA sequence design
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- benchmark research
- review date: 2026-09-17; status: primary_comparison_tables_located; primary sources: evidence-expansion-r3design-2025-b49c9ad8; inspected locators: Table 1; XML table TB1; Table 2; XML table TB2; Table 3; XML table TB3; searched queries: R3Design: deep tertiary structure-based RNA sequence design and beyond 10.1093/bib/bbae682; gaps: complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.; exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.; claim scope: Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
- historical missing metadata
- protocol version: 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
- benchmark
- entity classification
- review date: 2026-09-17; rationale: This source-scoped record identifies the biological prediction task and holds its paper context. Preserve the existing task identity; exact split, model adaptation and scoring remain in linked evaluations or separate protocol records.; source ids: r3design-2025; source locator: Results: benchmark dataset and structural assessment; cached text lines 10, 31–33; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.; Some legacy profile Entity type facts use the generic phrase computational evaluation protocol. That boilerplate is not sufficient to establish a single fixed protocol identity or to merge this task with another protocol record.
Related records
- dataset: Rfam
- benchmark: R3Design: RNA sequence design