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RTMScore rescoring of Protenix top-ranked poses

Ranks a compound library by the RTMScore deep-learning score, which prioritises the structural reliability of the pose computed on the top-ranked Protenix-predicted protein-ligand complex.

2 evaluations · 20 results

Overview

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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)
RTMScore rescoring of Protenix top-ranked posesEvaluation	GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3), GPCRrecent, 16 GPCR targets	0.644	Not reported	0.654	Not reported	0.08	Not reported	0.071	Not reported	4.17	Not reported	3.63	Not reported	3.66	Not reported	3.2	Not reported	2.69	Not reported	2.17	Not reported
RTMScore 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	0.852	Not reported	0.909	Not reported	0.64	Not reported	0.759	Not reported	21	Not reported	26.6	Not reported	20.4	Not reported	23.9	Not reported	11.6	Not reported	13

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: RTMScore 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	0.852 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 RTMScore 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 'RTMScore', column 'AUROC' (Mean)
Configuration: RTMScore 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	0.909 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 RTMScore 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 'RTMScore', column 'AUROC' (Med)
Configuration: RTMScore 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	0.64 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 RTMScore 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 'RTMScore', column 'BEDROC (α = 80.5)' (Mean)
Configuration: RTMScore 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	0.759 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 RTMScore 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 'RTMScore', column 'BEDROC (α = 80.5)' (Med)
Configuration: RTMScore 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	21 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 RTMScore 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 'RTMScore', column 'EF0.5%' (Mean)
Configuration: RTMScore 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	26.6 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 RTMScore 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 'RTMScore', column 'EF0.5%' (Med)
Configuration: RTMScore 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	20.4 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 RTMScore 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 'RTMScore', column 'EF1%' (Mean)
Configuration: RTMScore 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	23.9 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 RTMScore 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 'RTMScore', column 'EF1%' (Med)
Configuration: RTMScore 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	11.6 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 RTMScore 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 'RTMScore', column 'EF5%' (Mean)
Configuration: RTMScore 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	13 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 RTMScore 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 'RTMScore', column 'EF5%' (Med)
Configuration: RTMScore rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	0.644 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 (RTMScore) 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 (RTMScore)', column 'AUROC' (Mean)
Configuration: RTMScore rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	0.654 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 (RTMScore) 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 (RTMScore)', column 'AUROC' (Med)
Configuration: RTMScore rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	0.08 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 (RTMScore) 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 (RTMScore)', column 'BEDROC (α = 80.5)' (Mean)
Configuration: RTMScore rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	0.071 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 (RTMScore) 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 (RTMScore)', column 'BEDROC (α = 80.5)' (Med)
Configuration: RTMScore rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	4.17 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 (RTMScore) 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 (RTMScore)', column 'EF0.5%' (Mean)
Configuration: RTMScore rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	3.63 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 (RTMScore) 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 (RTMScore)', column 'EF0.5%' (Med)
Configuration: RTMScore rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	3.66 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 (RTMScore) 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 (RTMScore)', column 'EF1%' (Mean)
Configuration: RTMScore rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	3.2 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 (RTMScore) 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 (RTMScore)', column 'EF1%' (Med)
Configuration: RTMScore rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	2.69 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 (RTMScore) 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 (RTMScore)', column 'EF5%' (Mean)
Configuration: RTMScore rescoring of Protenix top-ranked poses	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	2.17 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 (RTMScore) 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 (RTMScore)', 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-rtmscore-on-protenix-poses

areas: molecular-interactions
contexts: research
method types: supervised_machine_learning
reported name: RTMScore
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
missing metadata: version: reason: unreported; note: The source states only that the official repository's inference script was used
provenance note: No entity-level record was created for this scoring function: its primary paper was not retrieved in this pass, so there is no source from which to describe it.

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