rewirebio.iobenchmarks
Evaluation

HelixFold3 on RNA complex hard set (LRMSD)

Published comparison transcribed from the pinned source; not reproduced.

Evaluation results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: HelixFold3 HelixFold3/73cd80b-hpc1 (Ludaic and Elofsson 2026 RNA benchmark run)Protocol: Ludaic and Elofsson 2026 RNA complex hard set, mean LRMSD
Dataset: Ludaic and Elofsson 2026 RNA complex hard set
48.6 CAPRI ligand RMSD
angstrom · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

HelixFold3 on RNA complex hard set (LRMSD)

lit-rna-20261011-rna3d-protocol-complex-hard-mean-lrmsd

Aggregation: Not reported

Limits of deep-learning-based RNA prediction methods · Table 5, row 'HF3', column 'LRMSD'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

Research readiness

0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified
  • Sample annotations are recorded: not yet verified
  • Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • A pinned run recipe exists: not yet verified
  • Compute requirements are estimated: not yet verified

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Independent validation data exist: not yet verified
  • Overlap with training data is checked: not yet verified

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Evaluation procedure

Ludaic and Elofsson 2026 RNA complex hard set, mean LRMSD

Configuration
HelixFold3 HelixFold3/73cd80b-hpc1 (Ludaic and Elofsson 2026 RNA benchmark run)
Protocol
Ludaic and Elofsson 2026 RNA complex hard set, mean LRMSD
Dataset
Ludaic and Elofsson 2026 RNA complex hard set
origin
Independent external evaluation
configuration
Primary source as retrieved 2026-10-11
protocol id
lit-rna-20261011-rna3d-protocol-complex-hard-mean-lrmsd
dataset version
PDB after training cut-offs, downloaded January 2026
split
Hard
population
Not reported
inputs
Sequence plus shared externally supplied MSAs where the method accepts them
adaptation
Default settings, no retraining; top-ranked of five models
metric implementation
DockQ
aggregation
Mean over targets
budget
Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split
Hard
Adaptation
Default settings, no retraining; top-ranked of five models
Scoring implementation
DockQ

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

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.

18 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statementOriginal source and locationReview and provenance
Comparison: adaptation
Default settings, no retraining; top-ranked of five models
Context-only references
Limits of deep-learning-based RNA prediction methods

Original source ↗

Table 5, row 'HF3', column 'LRMSD'

Version: Nucleic Acids Research 2026, gkag813 (issue date 2026-08-01); PMC13501138 full-text XML
Retrieved: 2026-10-11T21:27:03Z

not individually reviewed

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: 02043b4a3edbb62101f6abbca56c896a63fa5c7dc0c3956c58164daff015ad1f

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

Inspected artifact

Comparison: aggregation
Mean over targets
Context-only references
Limits of deep-learning-based RNA prediction methods

Original source ↗

Table 5, row 'HF3', column 'LRMSD'

Version: Nucleic Acids Research 2026, gkag813 (issue date 2026-08-01); PMC13501138 full-text XML
Retrieved: 2026-10-11T21:27:03Z

not individually reviewed

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: 02043b4a3edbb62101f6abbca56c896a63fa5c7dc0c3956c58164daff015ad1f

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

Inspected artifact

Comparison: budget
Not reported
Context-only references
Limits of deep-learning-based RNA prediction methods

Original source ↗

Table 5, row 'HF3', column 'LRMSD'

Version: Nucleic Acids Research 2026, gkag813 (issue date 2026-08-01); PMC13501138 full-text XML
Retrieved: 2026-10-11T21:27:03Z

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: 02043b4a3edbb62101f6abbca56c896a63fa5c7dc0c3956c58164daff015ad1f

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

Inspected artifact

Comparison: dataset version
PDB after training cut-offs, downloaded January 2026
Context-only references
Limits of deep-learning-based RNA prediction methods

Original source ↗

Table 5, row 'HF3', column 'LRMSD'

Version: Nucleic Acids Research 2026, gkag813 (issue date 2026-08-01); PMC13501138 full-text XML
Retrieved: 2026-10-11T21:27:03Z

not individually reviewed

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.dataset_version

Source artifact SHA-256: 02043b4a3edbb62101f6abbca56c896a63fa5c7dc0c3956c58164daff015ad1f

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

Inspected artifact

Comparison: inputs
Sequence plus shared externally supplied MSAs where the method accepts them
Context-only references
Limits of deep-learning-based RNA prediction methods

Original source ↗

Table 5, row 'HF3', column 'LRMSD'

Version: Nucleic Acids Research 2026, gkag813 (issue date 2026-08-01); PMC13501138 full-text XML
Retrieved: 2026-10-11T21:27:03Z

not individually reviewed

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.inputs

Source artifact SHA-256: 02043b4a3edbb62101f6abbca56c896a63fa5c7dc0c3956c58164daff015ad1f

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

Inspected artifact

Comparison: metric implementation
DockQ
Context-only references
Limits of deep-learning-based RNA prediction methods

Original source ↗

Table 5, row 'HF3', column 'LRMSD'

Version: Nucleic Acids Research 2026, gkag813 (issue date 2026-08-01); PMC13501138 full-text XML
Retrieved: 2026-10-11T21:27:03Z

not individually reviewed

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.metric_implementation

Source artifact SHA-256: 02043b4a3edbb62101f6abbca56c896a63fa5c7dc0c3956c58164daff015ad1f

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

Inspected artifact

Comparison: population
Not reported
Context-only references
Limits of deep-learning-based RNA prediction methods

Original source ↗

Table 5, row 'HF3', column 'LRMSD'

Version: Nucleic Acids Research 2026, gkag813 (issue date 2026-08-01); PMC13501138 full-text XML
Retrieved: 2026-10-11T21:27:03Z

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.population

Source artifact SHA-256: 02043b4a3edbb62101f6abbca56c896a63fa5c7dc0c3956c58164daff015ad1f

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

Inspected artifact

Comparison: protocol id
lit-rna-20261011-rna3d-protocol-complex-hard-mean-lrmsd
Context-only references
Limits of deep-learning-based RNA prediction methods

Original source ↗

Table 5, row 'HF3', column 'LRMSD'

Version: Nucleic Acids Research 2026, gkag813 (issue date 2026-08-01); PMC13501138 full-text XML
Retrieved: 2026-10-11T21:27:03Z

not individually reviewed

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.protocol_id

Source artifact SHA-256: 02043b4a3edbb62101f6abbca56c896a63fa5c7dc0c3956c58164daff015ad1f

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

Inspected artifact

Comparison: split
Hard
Context-only references
Limits of deep-learning-based RNA prediction methods

Original source ↗

Table 5, row 'HF3', column 'LRMSD'

Version: Nucleic Acids Research 2026, gkag813 (issue date 2026-08-01); PMC13501138 full-text XML
Retrieved: 2026-10-11T21:27:03Z

not individually reviewed

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.split

Source artifact SHA-256: 02043b4a3edbb62101f6abbca56c896a63fa5c7dc0c3956c58164daff015ad1f

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

Inspected artifact

Origin
independent_paper
Context-only references
Limits of deep-learning-based RNA prediction methods

Original source ↗

Table 5, row 'HF3', column 'LRMSD'

Version: Nucleic Acids Research 2026, gkag813 (issue date 2026-08-01); PMC13501138 full-text XML
Retrieved: 2026-10-11T21:27:03Z

not individually reviewed

No individual claim review recorded

independent paper

Audit details

Field: attributes.origin

Source artifact SHA-256: 02043b4a3edbb62101f6abbca56c896a63fa5c7dc0c3956c58164daff015ad1f

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

Inspected artifact

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: lit-rna-20261011-rna3d-eval-hf3-complex-hard-mean-lrmsd

areas
rna-transcriptomes; protein-structure
contexts
research
origin
independent_paper
protocol
lit-rna-20261011-rna3d-protocol-complex-hard-mean-lrmsd
version
Primary source as retrieved 2026-10-11
comparison
protocol id: lit-rna-20261011-rna3d-protocol-complex-hard-mean-lrmsd; dataset version: PDB after training cut-offs, downloaded January 2026; split: Hard; population: Not reported; inputs: Sequence plus shared externally supplied MSAs where the method accepts them; adaptation: Default settings, no retraining; top-ranked of five models; metric implementation: DockQ; aggregation: Mean over targets; budget: Not reported
source locator
Table 5, row 'HF3', column 'LRMSD'
missing metadata
comparison.budget: reason: unreported; comparison.population: reason: unreported
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