rewirebio.iobenchmarks
Evaluation

Boltz Rc · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95

Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries; Plinder-L95. Source checked, not independently reproduced.

Evaluation results

1 evaluation · 5 results. Different protocols are not a single leaderboard.

Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding · Dataset subset: Plinder-L95

Sorted by Bond angle RMSD (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configurationBond angle RMSDBond length RMSD (median over complexes)Chirality consistencyLigand RMSD (median over complexes; pocket superposition (residues within 10 A))RMSD (protein; median over complexes; atom set not stated)
Boltz RcEvaluation0.30.0215100%1.270.407
All 5 result rows with coverage, uncertainty and sources
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Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: Boltz RcProtocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding
Dataset subset: Plinder-L95
0.3 Bond angle RMSD
degree · lower

Uncertainty: Not yet extracted

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

Boltz Rc · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95

Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries

Aggregation: unreported in Table 1 footnote

Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz Rc; column angle_rmsd; footnote a
Configuration: Boltz RcProtocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding
Dataset subset: Plinder-L95
0.407 RMSD (protein; median over complexes; atom set not stated)
angstrom · lower

Uncertainty: Not yet extracted

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

Boltz Rc · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95

Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries

Aggregation: median

Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz Rc; column protein_rmsd; footnote a
Configuration: Boltz RcProtocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding
Dataset subset: Plinder-L95
0.0215 Bond length RMSD (median over complexes)
angstrom · lower

Uncertainty: Not yet extracted

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

Boltz Rc · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95

Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries

Aggregation: median

Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz Rc; column bond_rmsd; footnote a
Configuration: Boltz RcProtocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding
Dataset subset: Plinder-L95
1.27 Ligand RMSD (median over complexes; pocket superposition (residues within 10 A))
angstrom · lower

Uncertainty: Not yet extracted

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

Boltz Rc · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95

Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries

Aggregation: median

Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz Rc; column ligand_rmsd; footnote a
Configuration: Boltz RcProtocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding
Dataset subset: Plinder-L95
100% Chirality consistency
percent · higher

Uncertainty: Not yet extracted

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

Boltz Rc · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95

Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries

Aggregation: percentage of molecules with consistent chirality

Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz Rc; column chirality; footnote a

Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.

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 2026-11-02-a7f03c9e55a5 · 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

Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries

Configuration
Boltz Rc
Protocol
Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding
Dataset subset
Plinder-L95
origin
Author-reported evaluation
configuration
Not reported
protocol id
acquired-protocol-127e215c861a6b462f4d
dataset version
ACS Omega 2025 version of record; PMC12658688 XML retrieved 2026-09-19
split
all entries (includes Before and After training cutoff subsets)
population
Plinder-L95
inputs
co-folding
adaptation
unreported
aggregation
metric-specific; inspect each result

Metadata review: discovered. Unreported conditions prevent automatic comparisons.

Reproduction

Split
all entries (includes Before and After training cutoff subsets)
Adaptation
unreported
Scoring implementation
Not reported

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.

26 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statementOriginal source and locationReview and provenance
Comparison: adaptation
unreported
Context-only references
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction

Original source ↗

Table 1 (XML tbl1); row Boltz Rc; column protein_rmsd; footnote a

Version: version of record
Retrieved: 2026-09-16T10:41:16.555674+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: 78a77b9a0ab8bfa371f5b9baef3f443f4590d6e71cf864d67e90e9ebdfa7fc1b

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

Inspected artifact

Comparison: aggregation
metric-specific; inspect each result
Context-only references
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction

Original source ↗

Table 1 (XML tbl1); row Boltz Rc; column protein_rmsd; footnote a

Version: version of record
Retrieved: 2026-09-16T10:41:16.555674+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: 78a77b9a0ab8bfa371f5b9baef3f443f4590d6e71cf864d67e90e9ebdfa7fc1b

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

Inspected artifact

Comparison: dataset version
ACS Omega 2025 version of record; PMC12658688 XML retrieved 2026-09-19
Context-only references
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction

Original source ↗

Table 1 (XML tbl1); row Boltz Rc; column protein_rmsd; footnote a

Version: version of record
Retrieved: 2026-09-16T10:41:16.555674+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.dataset_version

Source artifact SHA-256: 78a77b9a0ab8bfa371f5b9baef3f443f4590d6e71cf864d67e90e9ebdfa7fc1b

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

Inspected artifact

Comparison: inputs
co-folding
Context-only references
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction

Original source ↗

Table 1 (XML tbl1); row Boltz Rc; column protein_rmsd; footnote a

Version: version of record
Retrieved: 2026-09-16T10:41:16.555674+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.inputs

Source artifact SHA-256: 78a77b9a0ab8bfa371f5b9baef3f443f4590d6e71cf864d67e90e9ebdfa7fc1b

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

Inspected artifact

Comparison: population
Plinder-L95
Context-only references
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction

Original source ↗

Table 1 (XML tbl1); row Boltz Rc; column protein_rmsd; footnote a

Version: version of record
Retrieved: 2026-09-16T10:41:16.555674+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.population

Source artifact SHA-256: 78a77b9a0ab8bfa371f5b9baef3f443f4590d6e71cf864d67e90e9ebdfa7fc1b

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

Inspected artifact

Comparison: protocol id
acquired-protocol-127e215c861a6b462f4d
Context-only references
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction

Original source ↗

Table 1 (XML tbl1); row Boltz Rc; column protein_rmsd; footnote a

Version: version of record
Retrieved: 2026-09-16T10:41:16.555674+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.protocol_id

Source artifact SHA-256: 78a77b9a0ab8bfa371f5b9baef3f443f4590d6e71cf864d67e90e9ebdfa7fc1b

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

Inspected artifact

Comparison: split
all entries (includes Before and After training cutoff subsets)
Context-only references
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction

Original source ↗

Table 1 (XML tbl1); row Boltz Rc; column protein_rmsd; footnote a

Version: version of record
Retrieved: 2026-09-16T10:41:16.555674+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.split

Source artifact SHA-256: 78a77b9a0ab8bfa371f5b9baef3f443f4590d6e71cf864d67e90e9ebdfa7fc1b

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

Inspected artifact

Conditions: checkpoint hash
Not reported
Context-only references
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction

Original source ↗

Table 1 (XML tbl1); row Boltz Rc; column protein_rmsd; footnote a

Version: version of record
Retrieved: 2026-09-16T10:41:16.555674+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.conditions.checkpoint_hash

Source artifact SHA-256: 78a77b9a0ab8bfa371f5b9baef3f443f4590d6e71cf864d67e90e9ebdfa7fc1b

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

Inspected artifact

Conditions: comparison compatibility
mixed_input_information; descriptive source table only, no ranked fair-comparison claim
Context-only references
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction

Original source ↗

Table 1 (XML tbl1); row Boltz Rc; column protein_rmsd; footnote a

Version: version of record
Retrieved: 2026-09-16T10:41:16.555674+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.conditions.comparison_compatibility

Source artifact SHA-256: 78a77b9a0ab8bfa371f5b9baef3f443f4590d6e71cf864d67e90e9ebdfa7fc1b

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

Inspected artifact

Conditions: dataset size
6600
Context-only references
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction

Original source ↗

Table 1 (XML tbl1); row Boltz Rc; column protein_rmsd; footnote a

Version: version of record
Retrieved: 2026-09-16T10:41:16.555674+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.conditions.dataset_size

Source artifact SHA-256: 78a77b9a0ab8bfa371f5b9baef3f443f4590d6e71cf864d67e90e9ebdfa7fc1b

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

Inspected artifact

How to read the evidence

Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: discovered

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

Stable ID: acquired-evaluation-a3eac23ea7ce1953b5e2

origin
author_reported
protocol
Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries
source locator
Table 1 (XML tbl1); row Boltz Rc; column protein_rmsd; footnote a
conditions
checkpoint hash: Not reported; comparison compatibility: mixed_input_information; descriptive source table only, no ranked fair-comparison claim; dataset size: 6600; eligible count: Not reported; input information: Vina receives ground-truth ligand-centred 30 angstrom cubic search box and exhaustiveness 16; neural co-folding methods receive shared MMSeqs2 v15 MSAs; input conditions differ.; model configuration: Boltz recycle=10, diffusion samples=5; AF3 and DiffDock default parameters; restraint variants as table condition.; plinder release: unextracted; restraint parameters: σstart = 1, w chiral = 1, w geom = 0; scored count: Not reported; selection: monomer proteins; single nonpolymeric ligand with sp3-carbon chiral center; allowed elements C,N,O,F,P,S,Cl,Br,I; RDKit conformer generation; ligand Tanimoto clustering 0.95; training overlap: All-entry summary includes structures before 2021-09-30; do not label held-out generalization.
comparison
protocol id: acquired-protocol-127e215c861a6b462f4d; dataset version: ACS Omega 2025 version of record; PMC12658688 XML retrieved 2026-09-19; split: all entries (includes Before and After training cutoff subsets); population: Plinder-L95; inputs: co-folding; adaptation: unreported; aggregation: metric-specific; inspect each result
missing metadata
checkpoint revision: reason: unreported; scored count: reason: unreported
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