Configuration

Gnina (CNNscore) rescoring of Protenix top-ranked poses

Ranks a compound library by Gnina's CNNscore convolutional neural network pose score computed on the top-ranked Protenix-predicted protein-ligand complex.

2 evaluations · 20 results

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

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 (CNNscore) rescoring of Protenix top-ranked posesEvaluation	GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3), GPCRrecent, 16 GPCR targets	0.652	Not reported	0.663	Not reported	0.118	Not reported	0.099	Not reported	7.37	Not reported	6.62	Not reported	5.8	Not reported	4.92	Not reported	3.38	Not reported	2.86	Not reported
Gnina (CNNscore) 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	0.846	Not reported	0.89	Not reported	0.515	Not reported	0.597	Not reported	18.1	Not reported	22.1	Not reported	16.7	Not reported	19.1	Not reported	9.34	Not reported	10

All 20 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Gnina (CNNscore) 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	0.846 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 (CNNscore) 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 (CNNscore)', column 'AUROC' (Mean)
Configuration: Gnina (CNNscore) 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	0.89 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 (CNNscore) 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 (CNNscore)', column 'AUROC' (Med)
Configuration: Gnina (CNNscore) 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	0.515 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 (CNNscore) 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 (CNNscore)', column 'BEDROC (α = 80.5)' (Mean)
Configuration: Gnina (CNNscore) 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	0.597 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 (CNNscore) 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 (CNNscore)', column 'BEDROC (α = 80.5)' (Med)
Configuration: Gnina (CNNscore) 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	18.1 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 (CNNscore) 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 (CNNscore)', column 'EF0.5%' (Mean)
Configuration: Gnina (CNNscore) 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	22.1 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 (CNNscore) 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 (CNNscore)', column 'EF0.5%' (Med)
Configuration: Gnina (CNNscore) 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	16.7 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 (CNNscore) 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 (CNNscore)', column 'EF1%' (Mean)
Configuration: Gnina (CNNscore) 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	19.1 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 (CNNscore) 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 (CNNscore)', column 'EF1%' (Med)
Configuration: Gnina (CNNscore) 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	9.34 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 (CNNscore) 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 (CNNscore)', column 'EF5%' (Mean)
Configuration: Gnina (CNNscore) 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	10 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 (CNNscore) 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 (CNNscore)', column 'EF5%' (Med)
Configuration: Gnina (CNNscore) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	0.652 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 (CNNscore) 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 (CNNscore)', column 'AUROC' (Mean)
Configuration: Gnina (CNNscore) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	0.663 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 (CNNscore) 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 (CNNscore)', column 'AUROC' (Med)
Configuration: Gnina (CNNscore) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	0.118 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 (CNNscore) 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 (CNNscore)', column 'BEDROC (α = 80.5)' (Mean)
Configuration: Gnina (CNNscore) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	0.099 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 (CNNscore) 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 (CNNscore)', column 'BEDROC (α = 80.5)' (Med)
Configuration: Gnina (CNNscore) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	7.37 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 (CNNscore) 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 (CNNscore)', column 'EF0.5%' (Mean)
Configuration: Gnina (CNNscore) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	6.62 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 (CNNscore) 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 (CNNscore)', column 'EF0.5%' (Med)
Configuration: Gnina (CNNscore) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	5.8 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 (CNNscore) 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 (CNNscore)', column 'EF1%' (Mean)
Configuration: Gnina (CNNscore) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	4.92 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 (CNNscore) 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 (CNNscore)', column 'EF1%' (Med)
Configuration: Gnina (CNNscore) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	3.38 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 (CNNscore) 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 (CNNscore)', column 'EF5%' (Mean)
Configuration: Gnina (CNNscore) rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	2.86 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 (CNNscore) 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 (CNNscore)', column 'EF5%' (Med)

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

Use this configuration

How it works, versions and access

Strengths, limitations and unresolved questions

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.

0 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

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

Sources and history

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

1 source record and release history

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

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: hitdisc-20261022-config-rescore-gnina-cnnscore-on-protenix-poses

areas: molecular-interactions
contexts: research
method types: supervised_machine_learning
reported name: Gnina (CNNscore)
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 (CNNscore) on Protenix-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2)
system: Protenix (CNNscore) on GPCRrecent (Shen et al. 2025 Table 3)

Suggest a correction