rewire.it
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

R1117: Sum of Z-scores for GDT-TS and TM-score. Scored with Sum of Z-scores for GDT-TS and TM-score on CASP15 natural RNA target R1117. 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.

10 evaluations · 10 metric rows

Overview

R1117: Sum of Z-scores for GDT-TS and TM-score. Scored with Sum of Z-scores for GDT-TS and TM-score on CASP15 natural RNA target R1117. 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.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Results

Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.

RhoFold+ 2024 CASP15 natural RNA comparison R1117-sum_z_gdt_ts_tm_score: R1117: Sum of Z-scores for GDT-TS and TM-score

sum_z_gdt_ts_tm_score (dimensionless) · Higher values are better.

Every method RhoFold+ 2024 CASP15 natural RNA comparison reports on R1117: Sum of Z-scores for GDT-TS and TM-score, scored with Sum of Z-scores for GDT-TS and TM-score on CASP15 natural RNA target R1117.

RhoFold+ 2024 CASP15 natural RNA comparison R1117-sum_z_gdt_ts_tm_score: R1117: Sum of Z-scores for GDT-TS and TM-score · CASP15 natural RNA target R1117 (RhoFold+ 2024 CASP15 natural RNA comparison split)

Evidence origin: Result quoted from another source, Independent external evaluation, Author-reported evaluation. Numerical source review does not establish independent reproduction.

RhoFold+ Nature Methods 2024: Source Data Figure 2h · Source Data Fig. 2, fig2hi!A1:M11, target R1117, Sum of Z-scores for GDT-TS and TM-score; Figure 2h caption; primary XML Par13–15 and Par51

Comparator configurations mix CASP15 expert/server submissions and retrospectively run published methods. These are not a controlled identical-compute benchmark.

All comparison limitations (10)
  • Comparator configurations mix CASP15 expert/server submissions and retrospectively run published methods. These are not a controlled identical-compute benchmark.
  • Best-of-five performance is not default single-prediction accuracy. Metric-specific candidate identity is not given in this sheet.
  • N/A is missing official data, never zero.
  • Do not pool target scores or infer an aggregate ranking from these extractions.
  • Numeric OOXML tokens can expose binary floating-point serialization; preserve raw tokens separately from numeric values and do not infer extra experimental precision.
  • Yang-best remains the workbook label; no inferred alias to a named model family.
  • The six natural targets are a bounded retrospective subset of CASP15, not the complete competition or a blind RhoFold+ submission.
  • All ten source rows and both metric blocks are retained. Eight N/A cells are preserved in source-cells.json and omitted from numerical result records.
  • Only source row RhoFold+ links to catalog-model-rhofold. Alchemy_RNA (RhoFold) and Alchemy_RNA2 are separate configurations.
  • CASP15 group scores are quoted prior submissions, not independent new experiments; AlphaFold3 is a third-party server evaluation reported by the RhoFold+ authors.

Automated source review: 2026-09-23.

No unavailable values; missing scores remain labelled and are never plotted as zero.

Showing 10 of 10 matching rows.

Tested configuration
-0.1120.9692.053.134.21
Reported score
  1. Chen3.98
  2. Alchemy_RNA23.91
  3. Alchemy_RNA (RhoFold)2.77
  4. RhoFold+2.0099999999999998
  5. AlphaFold31.97
  6. Yang-best1.54
  7. rDP (DRfold)1.1499999999999999
  8. DF_RNA (DeepFoldRNA)0.79
  9. UltraFold0.52
  10. Baker (RoseTTAFoldNA)0.12

Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Benchmarks

These source-backed links do not make different protocols or scores interchangeable.

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

Author-reported evaluations
1
External evaluations
1
paper compilation
8

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Protocol-valid structural control

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Thermodynamic folding with protocol-compatible input constraints

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums

Coverage is derived from release 2026-09-23-2b89723c6dd9. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

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

Claims, original sources and review scope · Release 2026-09-23-2b89723c6dd9
Property and statementOriginal source and locationReview and provenance
Relationship: part of
model-coverage-rhofold-casp15-natural
Individual claims		RhoFold+ Nature Methods 2024: Source Data Figure 2h

Original source ↗

Source Data Fig. 2, fig2hi!A1:M11, target R1117, Sum of Z-scores for GDT-TS and TM-score; Figure 2h caption; primary XML Par13–15 and Par51

Version: Publisher Source Data Fig. 2, DOI 10.1038/s41592-024-02487-0; retrieved 2026-09-23
Retrieved: 2026-09-23T11:23:43.985240+00:00

source checked

automated source review · 2026-09-23

Audit details

Primary-source transcription with no human sign-off and no independent reproduction.

Field: links:part_of:model-coverage-rhofold-casp15-natural

Claim: rhofold-2024-casp15-natural-association-r1117-sum-z-gdt-ts-tm-score

Source artifact SHA-256: 9d87837d6e72c8dafd265b9427c1cddd0223b3073eea26bcb4c6a90085a1bb04

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

All evidence (CSV)All evidence (JSONL)How to read the evidence

Sources and history

View linked audit checks and correction history

Release 2026-09-23-2b89723c6dd9 · Record review: source checked

1 source records and release historyDownload this release
Technical metadata and extraction receipts

Stable ID: rhofold-2024-casp15-natural-task-r1117-sum-z-gdt-ts-tm-score

areas
rna-transcriptomics
tasks
R1117: Sum of Z-scores for GDT-TS and TM-score
metric
Sum of Z-scores for GDT-TS and TM-score
metric direction
higher
dataset
CASP15 natural RNA target R1117
protocol
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.
source locator
Source Data Fig. 2, fig2hi!A1:M11, target R1117, Sum of Z-scores for GDT-TS and TM-score; Figure 2h caption; primary XML Par13–15 and Par51
comparison panels
id: rhofold-2024-casp15-natural-panel-r1117-sum-z-gdt-ts-tm-score; title: RhoFold+ 2024 CASP15 natural RNA comparison R1117-sum_z_gdt_ts_tm_score: R1117: Sum of Z-scores for GDT-TS and TM-score; protocol id: rhofold-2024-casp15-natural-task-r1117-sum-z-gdt-ts-tm-score; dataset id: rhofold-2024-casp15-natural-dataset-casp15-natural-rna-target-r1117; metric: sum_z_gdt_ts_tm_score; unit: dimensionless; direction: higher; result ids: rhofold-2024-casp15-natural-result-baker-rosettafoldna-r1117-sum-z-gdt-ts-tm-score-sum-z-gdt-ts-tm-score; rhofold-2024-casp15-natural-result-df-rna-deepfoldrna-r1117-sum-z-gdt-ts-tm-score-sum-z-gdt-ts-tm-score; rhofold-2024-casp15-natural-result-yang-best-r1117-sum-z-gdt-ts-tm-score-sum-z-gdt-ts-tm-score; rhofold-2024-casp15-natural-result-rdp-drfold-r1117-sum-z-gdt-ts-tm-score-sum-z-gdt-ts-tm-score; rhofold-2024-casp15-natural-result-ultrafold-r1117-sum-z-gdt-ts-tm-score-sum-z-gdt-ts-tm-score; rhofold-2024-casp15-natural-result-alchemy-rna-rhofold-r1117-sum-z-gdt-ts-tm-score-sum-z-gdt-ts-tm-score; rhofold-2024-casp15-natural-result-chen-r1117-sum-z-gdt-ts-tm-score-sum-z-gdt-ts-tm-score; rhofold-2024-casp15-natural-result-alchemy-rna2-r1117-sum-z-gdt-ts-tm-score-sum-z-gdt-ts-tm-score; rhofold-2024-casp15-natural-result-alphafold3-r1117-sum-z-gdt-ts-tm-score-sum-z-gdt-ts-tm-score; rhofold-2024-casp15-natural-result-rhofold-plus-r1117-sum-z-gdt-ts-tm-score-sum-z-gdt-ts-tm-score; source ids: model-coverage-rhofold-2024-fig2-source; source locator: Source Data Fig. 2, fig2hi!A1:M11, target R1117, Sum of Z-scores for GDT-TS and TM-score; Figure 2h caption; primary XML Par13–15 and Par51; context: Every method RhoFold+ 2024 CASP15 natural RNA comparison reports on R1117: Sum of Z-scores for GDT-TS and TM-score, scored with Sum of Z-scores for GDT-TS and TM-score on CASP15 natural RNA target R1117.; caveats: Comparator configurations mix CASP15 expert/server submissions and retrospectively run published methods. These are not a controlled identical-compute benchmark.; Best-of-five performance is not default single-prediction accuracy. Metric-specific candidate identity is not given in this sheet.; N/A is missing official data, never zero.; Do not pool target scores or infer an aggregate ranking from these extractions.; Numeric OOXML tokens can expose binary floating-point serialization; preserve raw tokens separately from numeric values and do not infer extra experimental precision.; Yang-best remains the workbook label; no inferred alias to a named model family.; The six natural targets are a bounded retrospective subset of CASP15, not the complete competition or a blind RhoFold+ submission.; All ten source rows and both metric blocks are retained. Eight N/A cells are preserved in source-cells.json and omitted from numerical result records.; Only source row RhoFold+ links to catalog-model-rhofold. Alchemy_RNA (RhoFold) and Alchemy_RNA2 are separate configurations.; CASP15 group scores are quoted prior submissions, not independent new experiments; AlphaFold3 is a third-party server evaluation reported by the RhoFold+ authors.; review: method: automated_source_review; date: 2026-09-23
entity level
protocol
Related records

Suggest a correction