Normalized enrichment factor (NEF at the top 1% of the ranked library, LIT-PCBA target MAPK1) of Gnina (CNNscore) docking baseline on LIT-PCBA five-target subset as scored by Shen et al. 2025
0.016 Normalized enrichment factor (NEF at the top 1% of the ranked library, LIT-PCBA target MAPK1)
Methods
- Tested configuration
- Gnina (CNNscore) 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
- Procedure
- LIT-PCBA five-target screening (Shen et al. 2025 Table 4)
- Evaluation
- Gnina (CNNscore) on the LIT-PCBA five-target subset (Shen et al. 2025 Table 4)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source: The source prints no interval or spread for this value
- Evidence
- Author-reported evaluation · source checkedShen et al. 2025, Chemical Science (Europe PMC full text) · Table 4, row 'Gnina (CNNscore)', column 'MAPK1' (NEF1%)
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- Five target sets, each with fewer than 100000 compounds; no training or test split applies
- Adaptation
- None; pretrained models and default or recommended settings
- Scoring implementation
- EF1% and NEF1%, where NEF1% is EF1% divided by its theoretical maximum at the 1% threshold
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 0.016 Individual claims | Shen et al. 2025, Chemical Science (Europe PMC full text) Table 4, row 'Gnina (CNNscore)', column 'MAPK1' (NEF1%) Version: PMC12704515 (Chem Sci, published 2025-12-11) | source checked ["independent-cell-check","deterministic-table-parse"] · 2026-10-22 author reported Audit detailsChecked against the pinned source by an automated independent re-parse. Transcription checked; not reproduced and not reviewed by a human scientist. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
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)
Technical metadata and extraction receipts
Stable ID: hitdisc-20261022-result-litpcba5-dock-gnina-cnnscore-mapk1-nef1
- metric
- normalized-enrichment-factor
- metric direction
- higher
- unit
- unitless
- metric qualifier
- NEF at the top 1% of the ranked library, LIT-PCBA target MAPK1
- printed value
- 0.016
- numeric value
- 0.016
- source locator
- Table 4, row 'Gnina (CNNscore)', column 'MAPK1' (NEF1%)
- missing metadata
- uncertainty: reason: unreported; note: The source prints no interval or spread for this value
- review
- method: independent-cell-check; deterministic-table-parse; reviewer: claude; reviewer note: Claude review agent, independent of the extraction agent; no human review claimed; date: 2026-10-22; method note: Re-downloaded the pinned Europe PMC XML, matched its SHA-256, and re-parsed Tables 1 to 5 with a parser written for this review (myparse_shen.py), independent of the extractor's build_batch.py. Every printed value, row label and column header compared; the parser was proved on six seeded errors.; note: Checked against the pinned source by an automated independent re-parse. 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
- source table
- Table 4
- source warnings
- Huang, Knight and Naprienko 2025 (arXiv:2507.21404v2, artifact e766c8aa4f94287672b2b1bacab2480a41ec7c806ecbaf5e2d1bf8773781310f, Abstract) audit LIT-PCBA and report extensive analogue and 2D-identical-compound leakage between its splits: 323 active training-validation analogue pairs at ECFP4 Tanimoto at or above 0.6 in ALDH1 alone and 2491 2D-identical inactives shared between training and validation across targets. They conclude that a parameter-free memorisation baseline matches or exceeds published deep-learning and 3D-similarity results, that nearly all published LIT-PCBA results are undermined, that zero-shot evaluations are also affected, and that the benchmark does not measure recovery of novel chemotypes. That bears on this value.; The actives-to-inactives ratio of LIT-PCBA is in dispute between the sources: the official page (artifact a2203612b553236d7f01da5573389d439d2f7aa0436080412f27da882e086e5e, data content table) gives 7761 actives and 382674 unique inactives for the 15 target sets, while Shen et al. 2025 (artifact 11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8, Methods 'Datasets') give 10030 confirmed actives and 2798737 confirmed inactives. Neither source reconciles the other. NEF1% is defined as a correction for that ratio, so the normalised values rest on a count the sources disagree about.