Configuration

Gnina (Vinardo) rescoring of AF3 top-ranked poses

Ranks a compound library by Gnina's classical Vinardo scoring function with the minimize option computed on the top-ranked AF3-predicted protein-ligand complex.

1 evaluation · 10 results

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Evaluations and results

1 evaluation · 10 results. Different protocols are not a single leaderboard.

Protocol: DEKOIS 2.0 screening by rescoring AF3-predicted complexes (Shen et al. 2025 Table 2, AF3 block) · Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025

Sorted by AUROC (AUROC, mean over the 79 DEKOIS 2.0 targets) (higher 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 configuration	AUROC (AUROC, mean over the 79 DEKOIS 2.0 targets)	AUROC (AUROC, median over the 79 DEKOIS 2.0 targets)	Bedroc (BEDROC with alpha = 80.5, mean over the 79 DEKOIS 2.0 targets)	Bedroc (BEDROC with alpha = 80.5, median over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 0.5% of the ranked library, mean over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 0.5% of the ranked library, median over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 1% of the ranked library, mean over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 1% of the ranked library, median over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 5% of the ranked library, mean over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 5% of the ranked library, median over the 79 DEKOIS 2.0 targets)
Gnina (Vinardo) rescoring of AF3 top-ranked posesEvaluation	0.757	0.766	0.27	0.239	9.19	8.86	8.45	7.15	5.21	4.5

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Gnina (Vinardo) rescoring of AF3 top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring AF3-predicted complexes (Shen et al. 2025 Table 2, AF3 block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.757 AUROC (AUROC, mean over the 79 DEKOIS 2.0 targets) 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 Gnina (Vinardo) on AF3-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-af3 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, AF3 block, row 'Gnina (Vinardo)', column 'AUROC' (Mean)
Configuration: Gnina (Vinardo) rescoring of AF3 top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring AF3-predicted complexes (Shen et al. 2025 Table 2, AF3 block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.766 AUROC (AUROC, median over the 79 DEKOIS 2.0 targets) 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 Gnina (Vinardo) on AF3-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-af3 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, AF3 block, row 'Gnina (Vinardo)', column 'AUROC' (Med)
Configuration: Gnina (Vinardo) rescoring of AF3 top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring AF3-predicted complexes (Shen et al. 2025 Table 2, AF3 block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.27 Bedroc (BEDROC with alpha = 80.5, mean over the 79 DEKOIS 2.0 targets) 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 Gnina (Vinardo) on AF3-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-af3 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, AF3 block, row 'Gnina (Vinardo)', column 'BEDROC (α = 80.5)' (Mean)
Configuration: Gnina (Vinardo) rescoring of AF3 top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring AF3-predicted complexes (Shen et al. 2025 Table 2, AF3 block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.239 Bedroc (BEDROC with alpha = 80.5, median over the 79 DEKOIS 2.0 targets) 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 Gnina (Vinardo) on AF3-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-af3 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, AF3 block, row 'Gnina (Vinardo)', column 'BEDROC (α = 80.5)' (Med)
Configuration: Gnina (Vinardo) rescoring of AF3 top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring AF3-predicted complexes (Shen et al. 2025 Table 2, AF3 block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	9.19 Enrichment factor (EF at the top 0.5% of the ranked library, mean over the 79 DEKOIS 2.0 targets) 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 Gnina (Vinardo) on AF3-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-af3 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, AF3 block, row 'Gnina (Vinardo)', column 'EF0.5%' (Mean)
Configuration: Gnina (Vinardo) rescoring of AF3 top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring AF3-predicted complexes (Shen et al. 2025 Table 2, AF3 block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	8.86 Enrichment factor (EF at the top 0.5% of the ranked library, median over the 79 DEKOIS 2.0 targets) 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 Gnina (Vinardo) on AF3-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-af3 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, AF3 block, row 'Gnina (Vinardo)', column 'EF0.5%' (Med)
Configuration: Gnina (Vinardo) rescoring of AF3 top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring AF3-predicted complexes (Shen et al. 2025 Table 2, AF3 block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	8.45 Enrichment factor (EF at the top 1% of the ranked library, mean over the 79 DEKOIS 2.0 targets) 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 Gnina (Vinardo) on AF3-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-af3 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, AF3 block, row 'Gnina (Vinardo)', column 'EF1%' (Mean)
Configuration: Gnina (Vinardo) rescoring of AF3 top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring AF3-predicted complexes (Shen et al. 2025 Table 2, AF3 block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	7.15 Enrichment factor (EF at the top 1% of the ranked library, median over the 79 DEKOIS 2.0 targets) 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 Gnina (Vinardo) on AF3-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-af3 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, AF3 block, row 'Gnina (Vinardo)', column 'EF1%' (Med)
Configuration: Gnina (Vinardo) rescoring of AF3 top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring AF3-predicted complexes (Shen et al. 2025 Table 2, AF3 block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	5.21 Enrichment factor (EF at the top 5% of the ranked library, mean over the 79 DEKOIS 2.0 targets) 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 Gnina (Vinardo) on AF3-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-af3 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, AF3 block, row 'Gnina (Vinardo)', column 'EF5%' (Mean)
Configuration: Gnina (Vinardo) rescoring of AF3 top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring AF3-predicted complexes (Shen et al. 2025 Table 2, AF3 block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	4.5 Enrichment factor (EF at the top 5% of the ranked library, median over the 79 DEKOIS 2.0 targets) 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 Gnina (Vinardo) on AF3-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-af3 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, AF3 block, row 'Gnina (Vinardo)', column 'EF5%' (Med)

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

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Shen et al. 2025, Chemical Science (Europe PMC full text) · Original source · PMC12704515 (Chem Sci, published 2025-12-11)

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Technical metadata and extraction receipts

Stable ID: hitdisc-20261022-config-rescore-gnina-vinardo-on-af3-poses

areas: molecular-interactions
contexts: research
method types: conventional_pipeline
reported name: Gnina (Vinardo)
configuration type: paper_evaluation
foundation model eligible: false
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: 11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12704515/fullTextXML; receipt: data/omics/use-case-coverage-hitdisc-20261022/review.json
parameters: Implementation set to default or recommended values; binding pockets defined from the predicted ligand pose
source locator: Methods 'Scoring schemes', 'Glide', 'Gnina', 'RTMScore, PIGNet2, PLANET and IGModel'
selection: Applied to the top-ranked of the five predicted poses, selected by the AF3 ranking score
version: Gnina version 1.3

Related records

configuration of: Gnina
system: Gnina (Vinardo) on AF3-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2)

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