rewirebio.iobenchmarks
Dataset

AmpC beta-lactamase docking hit list, 1293 tested compounds

The 1293 compounds from a 1.7-billion molecule DOCK3.7 screen against AmpC beta-lactamase that were synthesised and assayed, split into measured inhibitors and high-ranking docking false positives.

Evaluation results

3 evaluations · 3 results. Different protocols are not a single leaderboard.

Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: AF3 L-pLDDT (Kim, Correy, Hall et al. 2026 hit-list re-ranking)Protocol: Re-ranking the AmpC beta-lactamase docking hit list by co-folding and docking scores (Kim, Correy, Hall et al. 2026)
Dataset: AmpC beta-lactamase docking hit list, 1293 tested compounds
AUC = 60.5 AUROC (Discrimination of measured binders from high-ranking docking false positives in the tested AmpC beta-lactamase hit list)
unitless · higher

Uncertainty: Not reported by the source: The source prints no interval or spread for this value

Coverage: Not reported scored / Not reported eligible

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

AF3 L-pLDDT re-ranking the AmpC beta-lactamase docking hit list (Kim, Correy, Hall et al. 2026)

hitdisc-20261022-protocol-kim-ampc

Aggregation: Not reported

Kim, Correy, Hall et al. 2026, eLife 15:RP110475 (Europe PMC full text) · Results 'Co-folding struggles to reliably re-rank docking hit lists', paragraph on AmpC; printed in the body text as 'AUC = 60.5'
Configuration: Boltz-2 pIC50 (Kim, Correy, Hall et al. 2026 hit-list re-ranking)Protocol: Re-ranking the AmpC beta-lactamase docking hit list by co-folding and docking scores (Kim, Correy, Hall et al. 2026)
Dataset: AmpC beta-lactamase docking hit list, 1293 tested compounds
AUC = 68.1 AUROC (Discrimination of measured binders from high-ranking docking false positives in the tested AmpC beta-lactamase hit list)
unitless · higher

Uncertainty: Not reported by the source: The source prints no interval or spread for this value

Coverage: Not reported scored / Not reported eligible

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

Boltz-2 pIC50 re-ranking the AmpC beta-lactamase docking hit list (Kim, Correy, Hall et al. 2026)

hitdisc-20261022-protocol-kim-ampc

Aggregation: Not reported

Kim, Correy, Hall et al. 2026, eLife 15:RP110475 (Europe PMC full text) · Results 'Co-folding struggles to reliably re-rank docking hit lists', paragraph on AmpC; printed in the body text as 'AUC = 68.1'
Configuration: DOCK3.7 (Kim, Correy, Hall et al. 2026 hit-list re-ranking)Protocol: Re-ranking the AmpC beta-lactamase docking hit list by co-folding and docking scores (Kim, Correy, Hall et al. 2026)
Dataset: AmpC beta-lactamase docking hit list, 1293 tested compounds
AUC = 76.5 AUROC (Discrimination of measured binders from high-ranking docking false positives in the tested AmpC beta-lactamase hit list)
unitless · higher

Uncertainty: Not reported by the source: The source prints no interval or spread for this value

Coverage: Not reported scored / Not reported eligible

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

DOCK3.7 energy re-ranking the AmpC beta-lactamase docking hit list (Kim, Correy, Hall et al. 2026)

hitdisc-20261022-protocol-kim-ampc

Aggregation: Not reported

Kim, Correy, Hall et al. 2026, eLife 15:RP110475 (Europe PMC full text) · Results 'Co-folding struggles to reliably re-rank docking hit lists', paragraph on AmpC; printed in the body text as 'AUC = 76.5'

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.

Dataset and evaluation context

A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.

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.

12 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
Access
Supplementary file 5; hit lists from https://lsd.docking.org/
Context-only references
Kim, Correy, Hall et al. 2026, eLife 15:RP110475 (Europe PMC full text)

Original source ↗

Results 'Co-folding struggles to reliably re-rank docking hit lists'; Methods 'Benchmarking co-folding on experimentally validated compounds'

Version: PMC13657626 (eLife 2026;15:RP110475, version of record published 2026-10-12)
Retrieved: 2026-10-22T11:52:32Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.access

Source artifact SHA-256: 9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6

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

Assay
Enzyme inhibition, apparent Ki
Context-only references
Kim, Correy, Hall et al. 2026, eLife 15:RP110475 (Europe PMC full text)

Original source ↗

Results 'Co-folding struggles to reliably re-rank docking hit lists'; Methods 'Benchmarking co-folding on experimentally validated compounds'

Version: PMC13657626 (eLife 2026;15:RP110475, version of record published 2026-10-12)
Retrieved: 2026-10-22T11:52:32Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.assay

Source artifact SHA-256: 9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6

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

Label semantics
True hit: apparent Ki below 400 uM. The rest are non-binders, which are high-ranking docking false positives rather than property-matched decoys.
Context-only references
Kim, Correy, Hall et al. 2026, eLife 15:RP110475 (Europe PMC full text)

Original source ↗

Results 'Co-folding struggles to reliably re-rank docking hit lists'; Methods 'Benchmarking co-folding on experimentally validated compounds'

Version: PMC13657626 (eLife 2026;15:RP110475, version of record published 2026-10-12)
Retrieved: 2026-10-22T11:52:32Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.label_semantics

Source artifact SHA-256: 9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6

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

Negatives
1046
Context-only references
Kim, Correy, Hall et al. 2026, eLife 15:RP110475 (Europe PMC full text)

Original source ↗

Results 'Co-folding struggles to reliably re-rank docking hit lists'; Methods 'Benchmarking co-folding on experimentally validated compounds'

Version: PMC13657626 (eLife 2026;15:RP110475, version of record published 2026-10-12)
Retrieved: 2026-10-22T11:52:32Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.negatives

Source artifact SHA-256: 9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6

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

Population
1293 tested compounds sampled from scoring bins within the top-scoring 1% of 1.7 billion docked molecules: 247 true hits and 1046 non-binders
Context-only references
Kim, Correy, Hall et al. 2026, eLife 15:RP110475 (Europe PMC full text)

Original source ↗

Results 'Co-folding struggles to reliably re-rank docking hit lists'; Methods 'Benchmarking co-folding on experimentally validated compounds'

Version: PMC13657626 (eLife 2026;15:RP110475, version of record published 2026-10-12)
Retrieved: 2026-10-22T11:52:32Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.population

Source artifact SHA-256: 9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6

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

Positives
247
Context-only references
Kim, Correy, Hall et al. 2026, eLife 15:RP110475 (Europe PMC full text)

Original source ↗

Results 'Co-folding struggles to reliably re-rank docking hit lists'; Methods 'Benchmarking co-folding on experimentally validated compounds'

Version: PMC13657626 (eLife 2026;15:RP110475, version of record published 2026-10-12)
Retrieved: 2026-10-22T11:52:32Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.positives

Source artifact SHA-256: 9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6

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

Source location
Results 'Co-folding struggles to reliably re-rank docking hit lists'; Methods 'Benchmarking co-folding on experimentally validated compounds'
Context-only references
Kim, Correy, Hall et al. 2026, eLife 15:RP110475 (Europe PMC full text)

Original source ↗

Results 'Co-folding struggles to reliably re-rank docking hit lists'; Methods 'Benchmarking co-folding on experimentally validated compounds'

Version: PMC13657626 (eLife 2026;15:RP110475, version of record published 2026-10-12)
Retrieved: 2026-10-22T11:52:32Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.source_locator

Source artifact SHA-256: 9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6

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

Split
Whole tested set; no training or test split applies
Context-only references
Kim, Correy, Hall et al. 2026, eLife 15:RP110475 (Europe PMC full text)

Original source ↗

Results 'Co-folding struggles to reliably re-rank docking hit lists'; Methods 'Benchmarking co-folding on experimentally validated compounds'

Version: PMC13657626 (eLife 2026;15:RP110475, version of record published 2026-10-12)
Retrieved: 2026-10-22T11:52:32Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.split

Source artifact SHA-256: 9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6

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

Total
1293
Context-only references
Kim, Correy, Hall et al. 2026, eLife 15:RP110475 (Europe PMC full text)

Original source ↗

Results 'Co-folding struggles to reliably re-rank docking hit lists'; Methods 'Benchmarking co-folding on experimentally validated compounds'

Version: PMC13657626 (eLife 2026;15:RP110475, version of record published 2026-10-12)
Retrieved: 2026-10-22T11:52:32Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.total

Source artifact SHA-256: 9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6

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

Version
Compounds and measured potencies as provided in Supplementary file 5; the hit lists are available from https://lsd.docking.org/
Context-only references
Kim, Correy, Hall et al. 2026, eLife 15:RP110475 (Europe PMC full text)

Original source ↗

Results 'Co-folding struggles to reliably re-rank docking hit lists'; Methods 'Benchmarking co-folding on experimentally validated compounds'

Version: PMC13657626 (eLife 2026;15:RP110475, version of record published 2026-10-12)
Retrieved: 2026-10-22T11:52:32Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.version

Source artifact SHA-256: 9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6

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

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: hitdisc-20261022-dataset-kim-ampc

areas
molecular-interactions
contexts
research
version
Compounds and measured potencies as provided in Supplementary file 5; the hit lists are available from https://lsd.docking.org/
split
Whole tested set; no training or test split applies
population
1293 tested compounds sampled from scoring bins within the top-scoring 1% of 1.7 billion docked molecules: 247 true hits and 1046 non-binders
label semantics
True hit: apparent Ki below 400 uM. The rest are non-binders, which are high-ranking docking false positives rather than property-matched decoys.
positives
247
negatives
1046
total
1293
assay
Enzyme inhibition, apparent Ki
access
Supplementary file 5; hit lists from https://lsd.docking.org/
source locator
Results 'Co-folding struggles to reliably re-rank docking hit lists'; Methods 'Benchmarking co-folding on experimentally validated compounds'
review
method: scope-review; automated-source-review; reviewer: claude; reviewer note: Claude review agent, independent of the extraction agent; no human review claimed; date: 2026-10-22; method note: Read the record against the pinned sources and against docs/use-cases.md and docs/record-contract.md.; note: Record checked against the pinned source and the record contract. Transcription checked; not reproduced and not reviewed by a human scientist.; artifact sha256: 9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13657626/fullTextXML; receipt: data/omics/use-case-coverage-hitdisc-20261022/review.json
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