Protocol

LIT-PCBA five-target screening (Shen et al. 2025 Table 4)

Rank the experimentally measured actives and inactives of five LIT-PCBA targets with a co-folding confidence score or a docking baseline, and report the enrichment factor and the normalised enrichment factor at 1% per target and averaged.

7 evaluations · 84 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.

7 recorded evaluations, 84 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

7 evaluations · 84 results. Different protocols are not a single leaderboard.

Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) · Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025

Sorted by Enrichment factor (EF at the top 1% of the ranked library, averaged over the five 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	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)	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)
Boltz-2 (min-iPAE) as a screening scoreEvaluation	9.3 (best in column)	15.4 (best in column)	2.91	2.59	25.6 (best in column)	0	0.1 (best in column)	0.154 (best in column)	0.059	0.026	0.259 (best in column)	0
Boltz-2 (ipTM) as a screening scoreEvaluation	8.09	7.69	3.88	3.24 (best in column)	25.6 (best in column)	0	0.089	0.077	0.078	0.032 (best in column)	0.259 (best in column)	0
Protenix (ipTM) as a screening scoreEvaluation	7.58	7.69	1.94	1.3	22	5 (best in column)	0.089	0.077	0.039	0.013	0.222	0.093 (best in column)
Glide_SP docking baselineEvaluation	6.79	7.69	1.94	2.27	18.3	3.75	0.079	0.077	0.039	0.023	0.185	0.07
Gnina (CNNscore) docking baselineEvaluation	6.1	7.69	2.91	1.62	18.3	0	0.067	0.077	0.059	0.016	0.185	0
Gnina (CNNaffinity) docking baselineEvaluation	3.15	7.69	4.85 (best in column)	1.95	0	1.25	0.044	0.077	0.098 (best in column)	0.019	0	0.023
Gnina (Vina) docking baselineEvaluation	2.82	7.69	3.88	1.3	0	1.25	0.038	0.077	0.078	0.013	0	0.023

All 84 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: Boltz-2 (ipTM) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	8.09 Enrichment factor (EF at the top 1% of the ranked library, averaged over the five 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 Boltz-2 (ipTM) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (ipTM)', column 'Average' (EF1%)
Configuration: Boltz-2 (ipTM) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	0.089 Normalized enrichment factor (NEF at the top 1% of the ranked library, averaged over the five 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 Boltz-2 (ipTM) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (ipTM)', column 'Average' (NEF1%)
Configuration: Boltz-2 (ipTM) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	7.69 Enrichment factor (EF at the top 1% of the ranked library, LIT-PCBA target ESR_ago) 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 Boltz-2 (ipTM) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (ipTM)', column 'ESR_ago' (EF1%)
Configuration: Boltz-2 (ipTM) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	0.077 Normalized enrichment factor (NEF at the top 1% of the ranked library, LIT-PCBA target ESR_ago) 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 Boltz-2 (ipTM) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (ipTM)', column 'ESR_ago' (NEF1%)
Configuration: Boltz-2 (ipTM) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	3.88 Enrichment factor (EF at the top 1% of the ranked library, LIT-PCBA target ESR_antago) 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 Boltz-2 (ipTM) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (ipTM)', column 'ESR_antago' (EF1%)
Configuration: Boltz-2 (ipTM) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	0.078 Normalized enrichment factor (NEF at the top 1% of the ranked library, LIT-PCBA target ESR_antago) 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 Boltz-2 (ipTM) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (ipTM)', column 'ESR_antago' (NEF1%)
Configuration: Boltz-2 (ipTM) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	3.24 Enrichment factor (EF at the top 1% of the ranked library, LIT-PCBA target MAPK1) 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 Boltz-2 (ipTM) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (ipTM)', column 'MAPK1' (EF1%)
Configuration: Boltz-2 (ipTM) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	0.032 Normalized enrichment factor (NEF at the top 1% of the ranked library, LIT-PCBA target MAPK1) 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 Boltz-2 (ipTM) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (ipTM)', column 'MAPK1' (NEF1%)
Configuration: Boltz-2 (ipTM) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	25.6 Enrichment factor (EF at the top 1% of the ranked library, LIT-PCBA target PPARG) 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 Boltz-2 (ipTM) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (ipTM)', column 'PPARG' (EF1%)
Configuration: Boltz-2 (ipTM) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	0.259 Normalized enrichment factor (NEF at the top 1% of the ranked library, LIT-PCBA target PPARG) 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 Boltz-2 (ipTM) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (ipTM)', column 'PPARG' (NEF1%)
Configuration: Boltz-2 (ipTM) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	0 Enrichment factor (EF at the top 1% of the ranked library, LIT-PCBA target TP53) 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 Boltz-2 (ipTM) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (ipTM)', column 'TP53' (EF1%)
Configuration: Boltz-2 (ipTM) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	0 Normalized enrichment factor (NEF at the top 1% of the ranked library, LIT-PCBA target TP53) 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 Boltz-2 (ipTM) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (ipTM)', column 'TP53' (NEF1%)
Configuration: Boltz-2 (min-iPAE) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	9.3 Enrichment factor (EF at the top 1% of the ranked library, averaged over the five 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 Boltz-2 (min-iPAE) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (min-iPAE)', column 'Average' (EF1%)
Configuration: Boltz-2 (min-iPAE) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	0.1 Normalized enrichment factor (NEF at the top 1% of the ranked library, averaged over the five 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 Boltz-2 (min-iPAE) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (min-iPAE)', column 'Average' (NEF1%)
Configuration: Boltz-2 (min-iPAE) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	15.4 Enrichment factor (EF at the top 1% of the ranked library, LIT-PCBA target ESR_ago) 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 Boltz-2 (min-iPAE) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (min-iPAE)', column 'ESR_ago' (EF1%)
Configuration: Boltz-2 (min-iPAE) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	0.154 Normalized enrichment factor (NEF at the top 1% of the ranked library, LIT-PCBA target ESR_ago) 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 Boltz-2 (min-iPAE) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (min-iPAE)', column 'ESR_ago' (NEF1%)
Configuration: Boltz-2 (min-iPAE) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	2.91 Enrichment factor (EF at the top 1% of the ranked library, LIT-PCBA target ESR_antago) 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 Boltz-2 (min-iPAE) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (min-iPAE)', column 'ESR_antago' (EF1%)
Configuration: Boltz-2 (min-iPAE) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	0.059 Normalized enrichment factor (NEF at the top 1% of the ranked library, LIT-PCBA target ESR_antago) 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 Boltz-2 (min-iPAE) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (min-iPAE)', column 'ESR_antago' (NEF1%)
Configuration: Boltz-2 (min-iPAE) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	2.59 Enrichment factor (EF at the top 1% of the ranked library, LIT-PCBA target MAPK1) 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 Boltz-2 (min-iPAE) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (min-iPAE)', column 'MAPK1' (EF1%)
Configuration: Boltz-2 (min-iPAE) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	0.026 Normalized enrichment factor (NEF at the top 1% of the ranked library, LIT-PCBA target MAPK1) 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 Boltz-2 (min-iPAE) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (min-iPAE)', column 'MAPK1' (NEF1%)
Configuration: Boltz-2 (min-iPAE) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	25.6 Enrichment factor (EF at the top 1% of the ranked library, LIT-PCBA target PPARG) 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 Boltz-2 (min-iPAE) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (min-iPAE)', column 'PPARG' (EF1%)
Configuration: Boltz-2 (min-iPAE) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	0.259 Normalized enrichment factor (NEF at the top 1% of the ranked library, LIT-PCBA target PPARG) 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 Boltz-2 (min-iPAE) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (min-iPAE)', column 'PPARG' (NEF1%)
Configuration: Boltz-2 (min-iPAE) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	0 Enrichment factor (EF at the top 1% of the ranked library, LIT-PCBA target TP53) 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 Boltz-2 (min-iPAE) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (min-iPAE)', column 'TP53' (EF1%)
Configuration: Boltz-2 (min-iPAE) as a screening score	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	0 Normalized enrichment factor (NEF at the top 1% of the ranked library, LIT-PCBA target TP53) 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 Boltz-2 (min-iPAE) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Boltz-2 (min-iPAE)', column 'TP53' (NEF1%)
Configuration: Glide_SP docking baseline	Protocol: LIT-PCBA five-target screening (Shen et al. 2025 Table 4) Dataset: LIT-PCBA five-target subset as scored by Shen et al. 2025	6.79 Enrichment factor (EF at the top 1% of the ranked library, averaged over the five 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 Glide_SP on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4) hitdisc-20261022-protocol-shen-litpcba5 Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Glide_SP', column 'Average' (EF1%)

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

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

Author-reported evaluations: 7

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Protocol-specific valid geometric or structural control

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Upstream conventional structural reference with matched templates and cutoffs

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

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-protocol-shen-litpcba5

areas: molecular-interactions
contexts: research
task: Protein-ligand virtual screening (library ranking)
publication status: peer_reviewed
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
metric: enrichment-factor
metric direction: higher
unit: unitless
metric qualifier: EF at the top 1% of the ranked library, per target and averaged over the five targets
metric definition: EF1% is the ratio of true positives found in the top 1% of the ranked compounds relative to random selection. NEF1% is the observed EF1% divided by its theoretical maximum at that threshold, which confines it to [0, 1] and corrects for the different actives-to-inactives ratios between targets (Table 4 footnote a).
protocol: One structure selected from the recommended PDB entries per target for docking; ligands prepared with LigPrep; co-folding, Glide and Gnina applied to the same compounds.
denominator: 5
version: Shen et al. 2025, Table 4
source locator: Table 4 and footnote a
control: The actives and inactives are both experimentally measured, so the negatives are assayed rather than synthetic.
limitations: Enrichment factors depend on the actives-to-inactives ratio and on how the negatives were built, which differ by more than an order of magnitude between the benchmarks in this store (1:30 for DEKOIS 2.0, 1:50 for GPCRrecent, and from about 1:43 to about 1:200 across the five LIT-PCBA targets scored here, reaching about 1:18000 for LIT-PCBA ADRB2). Values from different protocols are not comparable.; Huang, Knight and Naprienko 2025 audit LIT-PCBA and conclude that analogue and 2D-identical-compound leakage between its splits lets a parameter-free memorisation baseline match or exceed published results, that nearly all published LIT-PCBA results are undermined, and that the benchmark does not measure recovery of novel chemotypes. That bears on every value from this protocol.; Five of the 15 LIT-PCBA targets were screened, chosen for size; MTORC1 meets the size criterion but was excluded for ambiguous binding sites, which is a selection the authors made rather than a property of the benchmark.; Only EF1% and NEF1% are printed for this table; no AUROC or BEDROC column is given.; AF3 was not run on this set.
scope note: Retrospective: the method ranks a curated set of actives and negatives that were assembled before the evaluation, not compounds selected and then tested.

Related records

evaluates task: Protein–ligand virtual screening
uses data: LIT-PCBA five-target subset as scored by Shen et al. 2025
part of: LIT-PCBA
assessment: Boltz-2 (ipTM) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4)
assessment: Boltz-2 (min-iPAE) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4)
assessment: Glide_SP on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4)
assessment: Gnina (CNNaffinity) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4)
assessment: Gnina (CNNscore) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4)
assessment: Gnina (Vina) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4)
assessment: Protenix (ipTM) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4)
used in: LIT-PCBA ESR_ago
used in: LIT-PCBA ESR_antago
used in: LIT-PCBA MAPK1
used in: LIT-PCBA PPARG
used in: LIT-PCBA TP53
subject: LIT-PCBA dataset subsets: used_in retargeted from a dataset to the protocol
assessed by: Find hits for a target by virtual screening

Suggest a correction