Configuration

Protenix (ipTM) as a screening score

Ranks a compound library by interface predicted template modeling score, covering only inter-chain interactions taken from the predicted protein-ligand complex.

4 evaluations · 42 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

4 evaluations · 42 results. Different protocols are not a single leaderboard.

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	Protocol and dataset	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)	AUROC (AUROC, mean over the 16 GPCRrecent targets)	AUROC (AUROC, median over the 16 GPCRrecent targets)	Bedroc (BEDROC with alpha = 80.5, mean over the 16 GPCRrecent targets)	Bedroc (BEDROC with alpha = 80.5, median over the 16 GPCRrecent 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, median over the 16 GPCRrecent targets)	Enrichment factor (EF at the top 1% of the ranked library, averaged over the five targets)	Enrichment factor (EF at the top 1% of the ranked library, LIT-PCBA target ESR_ago)	Enrichment factor (EF at the top 1% of the ranked library, LIT-PCBA target ESR_antago)	Enrichment factor (EF at the top 1% of the ranked library, LIT-PCBA target MAPK1)	Enrichment factor (EF at the top 1% of the ranked library, LIT-PCBA target PPARG)	Enrichment factor (EF at the top 1% of the ranked library, LIT-PCBA target TP53)	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, median over the 16 GPCRrecent 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, median over the 16 GPCRrecent targets)	Normalized enrichment factor (NEF at the top 1% of the ranked library, averaged over the five targets)	Normalized enrichment factor (NEF at the top 1% of the ranked library, LIT-PCBA target ESR_ago)	Normalized enrichment factor (NEF at the top 1% of the ranked library, LIT-PCBA target ESR_antago)	Normalized enrichment factor (NEF at the top 1% of the ranked library, LIT-PCBA target MAPK1)	Normalized enrichment factor (NEF at the top 1% of the ranked library, LIT-PCBA target PPARG)	Normalized enrichment factor (NEF at the top 1% of the ranked library, LIT-PCBA target TP53)
Protenix (ipTM) as a screening scoreEvaluation	DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1), DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.795 (best in column)	0.837 (best in column)	0.507 (best in column)	0.553 (best in column)	18.4 (best in column)	22.1 (best in column)	16.8 (best in column)	16.7 (best in column)	8.84 (best in column)	9.5 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Protenix (ipTM) as a screening scoreEvaluation	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	0.795 (best in column)	0.837 (best in column)	0.507 (best in column)	0.553 (best in column)	18.4 (best in column)	22.1 (best in column)	16.8 (best in column)	16.7 (best in column)	8.84 (best in column)	9.5 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Protenix (ipTM) as a screening scoreEvaluation	GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3), GPCRrecent, 16 GPCR targets	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.623	0.632	0.135	0.105	7.99	5.3	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	6.97	5.67	3.59	2.88	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Protenix (ipTM) as a screening scoreEvaluation	LIT-PCBA five-target screening (Shen et al. 2025 Table 4), LIT-PCBA five-target subset as scored by Shen et al. 2025	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	7.58	7.69	1.94	1.3	22	5	Not reported	Not reported	Not reported	Not reported	0.089	0.077	0.039	0.013	0.222	0.093

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Protenix (ipTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.795 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 Protenix (ipTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Protenix (ipTM)', column 'AUROC' (Mean)
Configuration: Protenix (ipTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.837 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 Protenix (ipTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Protenix (ipTM)', column 'AUROC' (Med)
Configuration: Protenix (ipTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.507 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 Protenix (ipTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Protenix (ipTM)', column 'BEDROC (α = 80.5)' (Mean)
Configuration: Protenix (ipTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.553 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 Protenix (ipTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Protenix (ipTM)', column 'BEDROC (α = 80.5)' (Med)
Configuration: Protenix (ipTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	18.4 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 Protenix (ipTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Protenix (ipTM)', column 'EF0.5%' (Mean)
Configuration: Protenix (ipTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) 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 Protenix (ipTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Protenix (ipTM)', column 'EF0.5%' (Med)
Configuration: Protenix (ipTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	16.8 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 Protenix (ipTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Protenix (ipTM)', column 'EF1%' (Mean)
Configuration: Protenix (ipTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) 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, 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 Protenix (ipTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Protenix (ipTM)', column 'EF1%' (Med)
Configuration: Protenix (ipTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	8.84 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 Protenix (ipTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Protenix (ipTM)', column 'EF5%' (Mean)
Configuration: Protenix (ipTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	9.5 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 Protenix (ipTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Protenix (ipTM)', column 'EF5%' (Med)
Configuration: Protenix (ipTM) as a screening score	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	0.795 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 ipTM 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 'ipTM', column 'AUROC' (Mean)
Configuration: Protenix (ipTM) as a screening score	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	0.837 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 ipTM 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 'ipTM', column 'AUROC' (Med)
Configuration: Protenix (ipTM) as a screening score	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	0.507 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 ipTM 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 'ipTM', column 'BEDROC (α = 80.5)' (Mean)
Configuration: Protenix (ipTM) as a screening score	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	0.553 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 ipTM 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 'ipTM', column 'BEDROC (α = 80.5)' (Med)
Configuration: Protenix (ipTM) as a screening score	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	18.4 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 ipTM 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 'ipTM', column 'EF0.5%' (Mean)
Configuration: Protenix (ipTM) as a screening score	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 ipTM 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 'ipTM', column 'EF0.5%' (Med)
Configuration: Protenix (ipTM) as a screening score	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	16.8 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 ipTM 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 'ipTM', column 'EF1%' (Mean)
Configuration: Protenix (ipTM) as a screening score	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, 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 ipTM 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 'ipTM', column 'EF1%' (Med)
Configuration: Protenix (ipTM) as a screening score	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	8.84 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 ipTM 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 'ipTM', column 'EF5%' (Mean)
Configuration: Protenix (ipTM) as a screening score	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	9.5 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 ipTM 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 'ipTM', column 'EF5%' (Med)
Configuration: Protenix (ipTM) as a screening score	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	0.623 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 (ipTM) 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 (ipTM)', column 'AUROC' (Mean)
Configuration: Protenix (ipTM) as a screening score	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	0.632 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 (ipTM) 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 (ipTM)', column 'AUROC' (Med)
Configuration: Protenix (ipTM) as a screening score	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	0.135 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 (ipTM) 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 (ipTM)', column 'BEDROC (α = 80.5)' (Mean)
Configuration: Protenix (ipTM) as a screening score	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	0.105 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 (ipTM) 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 (ipTM)', column 'BEDROC (α = 80.5)' (Med)
Configuration: Protenix (ipTM) as a screening score	Protocol: GPCRrecent screening (16 GPCR targets) (Shen et al. 2025 Table 3) Dataset: GPCRrecent, 16 GPCR targets	7.99 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 (ipTM) 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 (ipTM)', column 'EF0.5%' (Mean)

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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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Stable ID: hitdisc-20261022-config-protenix-iptm

areas: molecular-interactions
contexts: research
method types: foundation_model
reported name: Protenix (ipTM)
configuration type: paper_evaluation
foundation model eligible: true
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
version: Protenix version 0.4.4, five predictions with random seed 1, MMseqs2 web-service MSAs
access reuse: Source code at https://github.com/google-deepmind/alphafold3, https://github.com/bytedance/Protenix and https://github.com/jwohlwend/boltz (Data availability); no licence is stated in the source
parameters: All parameters other than the sample count and seed left at default or recommended values
score training overlap: Not assessed for this score by the source beyond the ligand-similarity analysis of Figure 5 and Fig. S10
source locator: Methods 'Complex structure prediction' and 'Scoring schemes'

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configuration of: Protenix
system: Protenix (ipTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1)
system: ipTM on Protenix-predicted DEKOIS 2.0 complexes (Shen et al. 2025 Table 2)
system: Protenix (ipTM) on GPCRrecent (Shen et al. 2025 Table 3)
system: Protenix (ipTM) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4)

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