Configuration

Gnina (AD4) rescoring of Protenix top-ranked poses

Ranks a compound library by Gnina's classical AD4 scoring function with the minimize option computed on the top-ranked Protenix-predicted protein-ligand complex.

2 evaluations · 20 results

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Evaluations and results

2 evaluations · 20 results. Different protocols are not a single leaderboard.

Sorted by AUROC (AUROC, mean over the 16 GPCRrecent 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	Protocol and dataset	AUROC (AUROC, mean over the 16 GPCRrecent targets)	AUROC (AUROC, mean over the 79 DEKOIS 2.0 targets)	AUROC (AUROC, median over the 16 GPCRrecent targets)	AUROC (AUROC, median over the 79 DEKOIS 2.0 targets)	Bedroc (BEDROC with alpha = 80.5, mean over the 16 GPCRrecent targets)	Bedroc (BEDROC with alpha = 80.5, mean over the 79 DEKOIS 2.0 targets)	Bedroc (BEDROC with alpha = 80.5, median over the 16 GPCRrecent 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 16 GPCRrecent 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 16 GPCRrecent 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 16 GPCRrecent 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 16 GPCRrecent 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 16 GPCRrecent 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 16 GPCRrecent targets)	Enrichment factor (EF at the top 5% of the ranked library, median over the 79 DEKOIS 2.0 targets)
Gnina (AD4) rescoring of Protenix top-ranked posesEvaluation	GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3), GPCRrecent, 16 GPCR targets	0.601	Not reported	0.594	Not reported	0.041	Not reported	0.038	Not reported	1.75	Not reported	1.32	Not reported	1.59	Not reported	1.41	Not reported	1.72	Not reported	1.72	Not reported
Gnina (AD4) rescoring of Protenix top-ranked posesEvaluation	DEKOIS 2.0 screening by rescoring Protenix-predicted complexes (Shen et al. 2025 Table 2, Protenix block), DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	Not reported	0.624	Not reported	0.607	Not reported	0.151	Not reported	0.108	Not reported	5.38	Not reported	4.43	Not reported	4.77	Not reported	2.38	Not reported	3.08	Not reported	2.5

All 20 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring Protenix-predicted complexes (Shen et al. 2025 Table 2, Protenix block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.624 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 (AD4) on Protenix-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-protenix Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, Protenix block, row 'Gnina (AD4)', column 'AUROC' (Mean)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring Protenix-predicted complexes (Shen et al. 2025 Table 2, Protenix block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.607 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 (AD4) on Protenix-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-protenix Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, Protenix block, row 'Gnina (AD4)', column 'AUROC' (Med)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring Protenix-predicted complexes (Shen et al. 2025 Table 2, Protenix block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.151 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 (AD4) on Protenix-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-protenix Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, Protenix block, row 'Gnina (AD4)', column 'BEDROC (α = 80.5)' (Mean)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring Protenix-predicted complexes (Shen et al. 2025 Table 2, Protenix block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.108 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 (AD4) on Protenix-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-protenix Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, Protenix block, row 'Gnina (AD4)', column 'BEDROC (α = 80.5)' (Med)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring Protenix-predicted complexes (Shen et al. 2025 Table 2, Protenix block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	5.38 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 (AD4) on Protenix-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-protenix Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, Protenix block, row 'Gnina (AD4)', column 'EF0.5%' (Mean)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring Protenix-predicted complexes (Shen et al. 2025 Table 2, Protenix block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	4.43 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 (AD4) on Protenix-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-protenix Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, Protenix block, row 'Gnina (AD4)', column 'EF0.5%' (Med)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring Protenix-predicted complexes (Shen et al. 2025 Table 2, Protenix block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	4.77 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 (AD4) on Protenix-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-protenix Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, Protenix block, row 'Gnina (AD4)', column 'EF1%' (Mean)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring Protenix-predicted complexes (Shen et al. 2025 Table 2, Protenix block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	2.38 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 (AD4) on Protenix-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-protenix Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, Protenix block, row 'Gnina (AD4)', column 'EF1%' (Med)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring Protenix-predicted complexes (Shen et al. 2025 Table 2, Protenix block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	3.08 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 (AD4) on Protenix-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-protenix Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, Protenix block, row 'Gnina (AD4)', column 'EF5%' (Mean)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: DEKOIS 2.0 screening by rescoring Protenix-predicted complexes (Shen et al. 2025 Table 2, Protenix block) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	2.5 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 (AD4) on Protenix-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2) hitdisc-20261022-protocol-shen-dekois-rescore-protenix Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 2, Protenix block, row 'Gnina (AD4)', column 'EF5%' (Med)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	0.601 AUROC (AUROC, mean over the 16 GPCRrecent 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 Protenix (AD4) on GPCRrecent (Shen et al. 2025 Table 3) hitdisc-20261022-protocol-shen-gpcrrecent-16 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 3, row 'Protenix (AD4)', column 'AUROC' (Mean)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	0.594 AUROC (AUROC, median over the 16 GPCRrecent 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 Protenix (AD4) on GPCRrecent (Shen et al. 2025 Table 3) hitdisc-20261022-protocol-shen-gpcrrecent-16 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 3, row 'Protenix (AD4)', column 'AUROC' (Med)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	0.041 Bedroc (BEDROC with alpha = 80.5, mean over the 16 GPCRrecent 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 Protenix (AD4) on GPCRrecent (Shen et al. 2025 Table 3) hitdisc-20261022-protocol-shen-gpcrrecent-16 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 3, row 'Protenix (AD4)', column 'BEDROC (α = 80.5)' (Mean)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	0.038 Bedroc (BEDROC with alpha = 80.5, median over the 16 GPCRrecent 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 Protenix (AD4) on GPCRrecent (Shen et al. 2025 Table 3) hitdisc-20261022-protocol-shen-gpcrrecent-16 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 3, row 'Protenix (AD4)', column 'BEDROC (α = 80.5)' (Med)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	1.75 Enrichment factor (EF at the top 0.5% of the ranked library, mean over the 16 GPCRrecent 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 Protenix (AD4) on GPCRrecent (Shen et al. 2025 Table 3) hitdisc-20261022-protocol-shen-gpcrrecent-16 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 3, row 'Protenix (AD4)', column 'EF0.5%' (Mean)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	1.32 Enrichment factor (EF at the top 0.5% of the ranked library, median over the 16 GPCRrecent 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 Protenix (AD4) on GPCRrecent (Shen et al. 2025 Table 3) hitdisc-20261022-protocol-shen-gpcrrecent-16 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 3, row 'Protenix (AD4)', column 'EF0.5%' (Med)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	1.59 Enrichment factor (EF at the top 1% of the ranked library, mean over the 16 GPCRrecent 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 Protenix (AD4) on GPCRrecent (Shen et al. 2025 Table 3) hitdisc-20261022-protocol-shen-gpcrrecent-16 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 3, row 'Protenix (AD4)', column 'EF1%' (Mean)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	1.41 Enrichment factor (EF at the top 1% of the ranked library, median over the 16 GPCRrecent 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 Protenix (AD4) on GPCRrecent (Shen et al. 2025 Table 3) hitdisc-20261022-protocol-shen-gpcrrecent-16 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 3, row 'Protenix (AD4)', column 'EF1%' (Med)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	1.72 Enrichment factor (EF at the top 5% of the ranked library, mean over the 16 GPCRrecent 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 Protenix (AD4) on GPCRrecent (Shen et al. 2025 Table 3) hitdisc-20261022-protocol-shen-gpcrrecent-16 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 3, row 'Protenix (AD4)', column 'EF5%' (Mean)
Configuration: Gnina (AD4) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	1.72 Enrichment factor (EF at the top 5% of the ranked library, median over the 16 GPCRrecent 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 Protenix (AD4) on GPCRrecent (Shen et al. 2025 Table 3) hitdisc-20261022-protocol-shen-gpcrrecent-16 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 3, row 'Protenix (AD4)', column 'EF5%' (Med)

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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-ad4-on-protenix-poses

areas: molecular-interactions
contexts: research
method types: conventional_pipeline
reported name: Gnina (AD4)
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 Protenix ranking score
version: Gnina version 1.3

Related records

configuration of: Gnina
system: Gnina (AD4) on Protenix-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2)
system: Protenix (AD4) on GPCRrecent (Shen et al. 2025 Table 3)

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