Evidence claim

Relevance of hitdisc-20261022-protocol-shen-litpcba5 to use-case-hit-discovery-virtual-screening

Evidence concern: excluded from comparisons

The official page (data content table, artifact a2203612b553236d7f01da5573389d439d2f7aa0436080412f27da882e086e5e) gives 7761 actives and 382674 unique inactives for the 15 LIT-PCBA target sets, while Shen et al. 2025 (Methods 'Datasets', artifact 11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8) state 10030 confirmed actives and 2798737 confirmed inactives for the full set. The two counts are not reconciled by either source; the difference is most likely unique against per-target inactives, but neither source says so. EF and NEF both depend on this ratio, so the conflict is left unresolved and marked rather than reconciled.LIT-PCBA official project page, drugdesign.unistra.fr · Official page data content table (artifact a2203612b553236d7f01da5573389d439d2f7aa0436080412f27da882e086e5e) against Shen et al. 2025 Methods 'Datasets' (artifact 11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8)

Use case: Find hits for a target by virtual screening
Assessed by: LIT-PCBA five-target screening (Shen et al. 2025 Table 4)
Relevance: Proxy evidence
Endpoint: Enrichment factor and normalised enrichment factor at the top 1% of the ranked library, per target and averaged over five targets

Relevance judgement drafted by the extraction agent. Not reviewed.

7 reviewed evaluations

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.

57 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
Citation locations 3 values source id hitdisc-20261022-source-shen2025 locator See the protocol record's source_locator source id hitdisc-20261022-source-litpcba-audit locator See the protocol record's source_locator source id hitdisc-20261022-source-litpcba-page locator See the protocol record's source_locator Context-only references	Huang, Knight and Naprienko 2025, arXiv:2507.21404v2 (abstract page) Original source ↗ hitdisc-20261022-protocol-shen-litpcba5: see its source_locator Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv:2507.21404v2, submitted 2025-07-29, this version 2025-08-07 Retrieved: 2026-10-22T11:59:20Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `e766c8aa4f94287672b2b1bacab2480a41ec7c806ecbaf5e2d1bf8773781310f` Hash scope: This is a mutable web page: artifact_sha256 describes the single retrieval of 2026-10-22T11:59:20Z and a later change to the page would change it.
Citation locations 3 values source id hitdisc-20261022-source-shen2025 locator See the protocol record's source_locator source id hitdisc-20261022-source-litpcba-audit locator See the protocol record's source_locator source id hitdisc-20261022-source-litpcba-page locator See the protocol record's source_locator Context-only references	LIT-PCBA official project page, drugdesign.unistra.fr Original source ↗ hitdisc-20261022-protocol-shen-litpcba5: see its source_locator Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Page as retrieved 2026-10-22; no version is printed on the page Retrieved: 2026-10-22T12:01:54Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `a2203612b553236d7f01da5573389d439d2f7aa0436080412f27da882e086e5e` Hash scope: This is a mutable web page: artifact_sha256 describes the single retrieval of 2026-10-22T12:01:54Z and a later change to the page would change it.
Citation locations 3 values source id hitdisc-20261022-source-shen2025 locator See the protocol record's source_locator source id hitdisc-20261022-source-litpcba-audit locator See the protocol record's source_locator source id hitdisc-20261022-source-litpcba-page locator See the protocol record's source_locator Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-litpcba5: see its source_locator Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12704515 (Chem Sci, published 2025-12-11) Retrieved: 2026-10-22T11:52:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
Comparison group screening-enrichment-measured-inactives Context-only references	Huang, Knight and Naprienko 2025, arXiv:2507.21404v2 (abstract page) Original source ↗ hitdisc-20261022-protocol-shen-litpcba5: see its source_locator Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv:2507.21404v2, submitted 2025-07-29, this version 2025-08-07 Retrieved: 2026-10-22T11:59:20Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `e766c8aa4f94287672b2b1bacab2480a41ec7c806ecbaf5e2d1bf8773781310f` Hash scope: This is a mutable web page: artifact_sha256 describes the single retrieval of 2026-10-22T11:59:20Z and a later change to the page would change it.
Comparison group screening-enrichment-measured-inactives Context-only references	LIT-PCBA official project page, drugdesign.unistra.fr Original source ↗ hitdisc-20261022-protocol-shen-litpcba5: see its source_locator Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Page as retrieved 2026-10-22; no version is printed on the page Retrieved: 2026-10-22T12:01:54Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `a2203612b553236d7f01da5573389d439d2f7aa0436080412f27da882e086e5e` Hash scope: This is a mutable web page: artifact_sha256 describes the single retrieval of 2026-10-22T12:01:54Z and a later change to the page would change it.
Comparison group screening-enrichment-measured-inactives Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-litpcba5: see its source_locator Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12704515 (Chem Sci, published 2025-12-11) Retrieved: 2026-10-22T11:52:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
Comparison title Retrospective enrichment where the inactives were measured Context-only references	Huang, Knight and Naprienko 2025, arXiv:2507.21404v2 (abstract page) Original source ↗ hitdisc-20261022-protocol-shen-litpcba5: see its source_locator Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv:2507.21404v2, submitted 2025-07-29, this version 2025-08-07 Retrieved: 2026-10-22T11:59:20Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `e766c8aa4f94287672b2b1bacab2480a41ec7c806ecbaf5e2d1bf8773781310f` Hash scope: This is a mutable web page: artifact_sha256 describes the single retrieval of 2026-10-22T11:59:20Z and a later change to the page would change it.
Comparison title Retrospective enrichment where the inactives were measured Context-only references	LIT-PCBA official project page, drugdesign.unistra.fr Original source ↗ hitdisc-20261022-protocol-shen-litpcba5: see its source_locator Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Page as retrieved 2026-10-22; no version is printed on the page Retrieved: 2026-10-22T12:01:54Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `a2203612b553236d7f01da5573389d439d2f7aa0436080412f27da882e086e5e` Hash scope: This is a mutable web page: artifact_sha256 describes the single retrieval of 2026-10-22T12:01:54Z and a later change to the page would change it.
Comparison title Retrospective enrichment where the inactives were measured Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-litpcba5: see its source_locator Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12704515 (Chem Sci, published 2025-12-11) Retrieved: 2026-10-22T11:52:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
Constraints 3 values Inspect every linked evaluation's source locator before citing a result. Compare rows only within this protocol. Enrichment factors from different protocols are not comparable, because the actives-to-inactives ratio and the construction of the negatives differ. Do not read a result from this protocol together with the Mac1 pose results or the CASF-2016 scoring, ranking and docking protocols already in this store: those measure pose and scoring accuracy, not the ranking of a library. Context-only references	Huang, Knight and Naprienko 2025, arXiv:2507.21404v2 (abstract page) Original source ↗ hitdisc-20261022-protocol-shen-litpcba5: see its source_locator Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv:2507.21404v2, submitted 2025-07-29, this version 2025-08-07 Retrieved: 2026-10-22T11:59:20Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `e766c8aa4f94287672b2b1bacab2480a41ec7c806ecbaf5e2d1bf8773781310f` Hash scope: This is a mutable web page: artifact_sha256 describes the single retrieval of 2026-10-22T11:59:20Z and a later change to the page would change it.

How to read the evidence

Sources and history

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

3 source records and release history

Shen et al. 2025, Chemical Science (Europe PMC full text) · Original source · PMC12704515 (Chem Sci, published 2025-12-11)
Huang, Knight and Naprienko 2025, arXiv:2507.21404v2 (abstract page) · Original source · arXiv:2507.21404v2, submitted 2025-07-29, this version 2025-08-07
LIT-PCBA official project page, drugdesign.unistra.fr · Original source · Page as retrieved 2026-10-22; no version is printed on the page

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Technical metadata and extraction receipts

Stable ID: hitdisc-20261022-use-case-mapping-shen-litpcba5

field: links:assessed_by:hitdisc-20261022-protocol-shen-litpcba5
value: hitdisc-20261022-protocol-shen-litpcba5
relevance: proxy
endpoint: Enrichment factor and normalised enrichment factor at the top 1% of the ranked library, per target and averaged over five targets
rationale: Proxy, and the most informative retrospective arm in the batch, because the inactives were experimentally measured rather than constructed. It is still proxy evidence: the compounds were chosen by past screening campaigns, the benchmark is retrospective, and its splits are compromised by the leakage the audit documents. The co-folding advantage over docking that the decoy benchmarks show largely disappears here: averaged over the five targets Boltz-2 min-iPAE gives EF1% 9.30 and NEF1% 0.100 against Glide SP's 6.79 and 0.079, and on TP53 both Boltz-2 scores give EF1% 0.00 while Protenix ipTM gives 5.00 and Glide SP 3.75.
constraints: Inspect every linked evaluation's source locator before citing a result.; Compare rows only within this protocol. Enrichment factors from different protocols are not comparable, because the actives-to-inactives ratio and the construction of the negatives differ.; Do not read a result from this protocol together with the Mac1 pose results or the CASF-2016 scoring, ranking and docking protocols already in this store: those measure pose and scoring accuracy, not the ranking of a library.
limitations: The LIT-PCBA leakage audit concludes that a parameter-free memorisation baseline matches or exceeds published deep-learning results on this benchmark and that nearly all published results on it are undermined. Every value from this protocol must be read with that finding.; Five of 15 targets were screened, selected for size, and MTORC1 was dropped for ambiguous binding sites.; No AUROC or BEDROC column is printed for this table, so early-recognition behaviour cannot be compared with the decoy benchmarks.; Transcribed from the source; no reproduction by Rewire and no human scientific review.; No ligand-similarity or pharmacophore baseline is scored on any protocol in this batch, although issue #177 asks for one as the pre-machine-learning comparator alongside docking.
citation locators: source id: hitdisc-20261022-source-shen2025; locator: See the protocol record's source_locator; source id: hitdisc-20261022-source-litpcba-audit; locator: See the protocol record's source_locator; source id: hitdisc-20261022-source-litpcba-page; locator: See the protocol record's source_locator
source locator: hitdisc-20261022-protocol-shen-litpcba5: see its source_locator
headline metric: enrichment-factor
comparison group: screening-enrichment-measured-inactives
comparison title: Retrospective enrichment where the inactives were measured
stratum label: LIT-PCBA, five targets under 100,000 compounds (7 arms)
stratum order: 1
reason: Hit-discovery use-case pass 2026-10-22: relevance of a protocol to a new use case (rewire-benchmark-data #177).
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: Claim checked against the pinned source. Every figure it states was matched to a result record in this batch.; 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
reviewed evaluations: hitdisc-20261022-eval-litpcba5-boltz2-iptm; hitdisc-20261022-eval-litpcba5-boltz2-minipae; hitdisc-20261022-eval-litpcba5-dock-glide-sp; hitdisc-20261022-eval-litpcba5-dock-gnina-cnnaffinity; hitdisc-20261022-eval-litpcba5-dock-gnina-cnnscore; hitdisc-20261022-eval-litpcba5-dock-gnina-vina; hitdisc-20261022-eval-litpcba5-protenix-iptm
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