Evaluation

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

Published result; transcribed, not reproduced.

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Tested configuration	Protocol and dataset	Finding	Evidence 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'

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Evaluation procedure

Re-ranking the AmpC beta-lactamase docking hit list by co-folding and docking scores (Kim, Correy, Hall et al. 2026)

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

origin: Author-reported evaluation
configuration: Not reported
protocol id: hitdisc-20261022-protocol-kim-ampc
dataset version: Tested compounds and measured potencies as provided in Supplementary file 5
split: Whole tested list; 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
inputs: Ligand SMILES and the protein sequence for the co-folding scores; the ligand SMILES and the receptor structure for DOCK3.7
adaptation: None; pretrained models and the published docking receptor
metric implementation: Area under the receiver operating characteristic curve for separating true hits from non-binders, printed as a percentage
aggregation: Pooled over the compounds of one target's tested list
budget: Not reported

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

Reproduction

Split: Whole tested list; no training or test split applies
Adaptation: None; pretrained models and the published docking receptor
Scoring implementation: Area under the receiver operating characteristic curve for separating true hits from non-binders, printed as a percentage

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Evidence

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Evidence table

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19 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Comparison: adaptation None; pretrained models and the published docking receptor 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', paragraph on AmpC 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 author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6` Hash scope: Hash scope not separately documented; inspect source record
Comparison: aggregation Pooled over the compounds of one target's tested list 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', paragraph on AmpC 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 author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6` Hash scope: Hash scope not separately documented; inspect source record
Comparison: budget Not reported 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', paragraph on AmpC Version: PMC13657626 (eLife 2026;15:RP110475, version of record published 2026-10-12) Retrieved: 2026-10-22T11:52:32Z	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6` Hash scope: Hash scope not separately documented; inspect source record
Comparison: dataset version Tested compounds and measured potencies as provided in Supplementary file 5 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', paragraph on AmpC 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 author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6` Hash scope: Hash scope not separately documented; inspect source record
Comparison: inputs Ligand SMILES and the protein sequence for the co-folding scores; the ligand SMILES and the receptor structure for DOCK3.7 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', paragraph on AmpC 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 author reported Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6` Hash scope: Hash scope not separately documented; inspect source record
Comparison: metric implementation Area under the receiver operating characteristic curve for separating true hits from non-binders, printed as a percentage 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', paragraph on AmpC 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 author reported Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6` Hash scope: Hash scope not separately documented; inspect source record
Comparison: 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', paragraph on AmpC 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 author reported Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6` Hash scope: Hash scope not separately documented; inspect source record
Comparison: protocol id hitdisc-20261022-protocol-kim-ampc 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', paragraph on AmpC 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 author reported Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6` Hash scope: Hash scope not separately documented; inspect source record
Comparison: split Whole tested list; 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', paragraph on AmpC 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 author reported Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6` Hash scope: Hash scope not separately documented; inspect source record
Interpretation The compounds were all synthesised and assayed, but the score comparison is a retrospective re-ranking of that tested set rather than a new prospective screen. 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', paragraph on AmpC 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 author reported Audit details Field: `attributes.interpretation` Source artifact SHA-256: `9be510b7b0cc152ff56a03c96877bf06b6a6bdeffdb4baecf8e999a6bf155aa6` Hash scope: Hash scope not separately documented; inspect source record

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Sources and history

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

1 source record and release history

Kim, Correy, Hall et al. 2026, eLife 15:RP110475 (Europe PMC full text) · Original source · PMC13657626 (eLife 2026;15:RP110475, version of record published 2026-10-12)

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Technical metadata and extraction receipts

Stable ID: hitdisc-20261022-eval-kim-ampc-kim-af3-lplddt

areas: molecular-interactions
contexts: research
origin: author_reported
protocol: hitdisc-20261022-protocol-kim-ampc
comparison: protocol id: hitdisc-20261022-protocol-kim-ampc; dataset version: Tested compounds and measured potencies as provided in Supplementary file 5; split: Whole tested list; 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; inputs: Ligand SMILES and the protein sequence for the co-folding scores; the ligand SMILES and the receptor structure for DOCK3.7; adaptation: None; pretrained models and the published docking receptor; metric implementation: Area under the receiver operating characteristic curve for separating true hits from non-binders, printed as a percentage; aggregation: Pooled over the compounds of one target's tested list; budget: Not reported
source locator: Results 'Co-folding struggles to reliably re-rank docking hit lists', paragraph on AmpC
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
missing metadata: comparison.budget: reason: unreported; note: No compute budget is stated for this arm
retrospective: true
interpretation: The compounds were all synthesised and assayed, but the score comparison is a retrospective re-ranking of that tested set rather than a new prospective screen.

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