Evidence claim

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

Use case: Find hits for a target by virtual screening
Assessed by: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1)
Relevance: Proxy evidence
Endpoint: AUROC, BEDROC (alpha = 80.5) and enrichment factors at 0.5%, 1% and 5%, mean and median over 79 DEKOIS 2.0 targets

Relevance judgement drafted by the extraction agent. Not reviewed.

24 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.

19 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 1 values source id hitdisc-20261022-source-shen2025 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-dekois-builtin: see its source_locator 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-synthetic-decoys Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-dekois-builtin: see its source_locator 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 on synthetic property-matched decoys Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-dekois-builtin: see its source_locator 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	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-dekois-builtin: see its source_locator 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.constraints` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
Endpoint AUROC, BEDROC (alpha = 80.5) and enrichment factors at 0.5%, 1% and 5%, mean and median over 79 DEKOIS 2.0 targets Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-dekois-builtin: see its source_locator 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.endpoint` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
Claimed field links:assessed_by:hitdisc-20261022-protocol-shen-dekois-builtin Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-dekois-builtin: see its source_locator 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.field` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
Headline metric enrichment-factor Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-dekois-builtin: see its source_locator 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.headline_metric` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
Limitations 4 values Eight of the 24 arms are values quoted from five other papers, so they were not produced under one common pipeline. The two Boltz-2 affinity arms are flagged by the authors themselves as likely over-estimates from training-data overlap with the databases that source DEKOIS 2.0. 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. Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-dekois-builtin: see its source_locator 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.limitations` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
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dc57177bbc7bd26bcb01b194ecc3598e987ff5dc02a07432c4585abfde8e97cc Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-dekois-builtin: see its source_locator 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.pins` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
Rationale Proxy: the endpoint is exactly the one the use case asks about, ranking a library so that real binders come out on top, and docking baselines are scored on the same targets and compounds. But the negatives are property-matched decoys selected from ZINC rather than compounds anyone assayed, so the enrichment figures measure separation from synthetic molecules, not from the false positives a real screen throws up. The best co-folding score here reaches EF1% 23.15 (AF3 min-iPAE, mean) against 12.01 for the quoted Glide SP row, a margin that does not survive the move to measured inactives in this same paper. Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-dekois-builtin: see its source_locator 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.rationale` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record

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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)

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Technical metadata and extraction receipts

Stable ID: hitdisc-20261022-use-case-mapping-shen-dekois-builtin

field: links:assessed_by:hitdisc-20261022-protocol-shen-dekois-builtin
value: hitdisc-20261022-protocol-shen-dekois-builtin
relevance: proxy
endpoint: AUROC, BEDROC (alpha = 80.5) and enrichment factors at 0.5%, 1% and 5%, mean and median over 79 DEKOIS 2.0 targets
rationale: Proxy: the endpoint is exactly the one the use case asks about, ranking a library so that real binders come out on top, and docking baselines are scored on the same targets and compounds. But the negatives are property-matched decoys selected from ZINC rather than compounds anyone assayed, so the enrichment figures measure separation from synthetic molecules, not from the false positives a real screen throws up. The best co-folding score here reaches EF1% 23.15 (AF3 min-iPAE, mean) against 12.01 for the quoted Glide SP row, a margin that does not survive the move to measured inactives in this same paper.
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: Eight of the 24 arms are values quoted from five other papers, so they were not produced under one common pipeline.; The two Boltz-2 affinity arms are flagged by the authors themselves as likely over-estimates from training-data overlap with the databases that source DEKOIS 2.0.; 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 locator: hitdisc-20261022-protocol-shen-dekois-builtin: see its source_locator
headline metric: enrichment-factor
comparison group: screening-enrichment-synthetic-decoys
comparison title: Retrospective enrichment on synthetic property-matched decoys
stratum label: DEKOIS 2.0, built-in co-folding scores against docking tools (24 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-dekois-builtin-af3-iptm; hitdisc-20261022-eval-dekois-builtin-af3-minipae; hitdisc-20261022-eval-dekois-builtin-af3-ptm; hitdisc-20261022-eval-dekois-builtin-af3-ranking; hitdisc-20261022-eval-dekois-builtin-boltz2-affinity; hitdisc-20261022-eval-dekois-builtin-boltz2-iptm; hitdisc-20261022-eval-dekois-builtin-boltz2-minipae; hitdisc-20261022-eval-dekois-builtin-boltz2-probability; hitdisc-20261022-eval-dekois-builtin-boltz2-ptm; hitdisc-20261022-eval-dekois-builtin-boltz2-ranking; hitdisc-20261022-eval-dekois-builtin-dock-gnina-cnnaffinity; hitdisc-20261022-eval-dekois-builtin-dock-gnina-cnnscore; hitdisc-20261022-eval-dekois-builtin-dock-gnina-vina; hitdisc-20261022-eval-dekois-builtin-protenix-iptm; hitdisc-20261022-eval-dekois-builtin-protenix-ptm; hitdisc-20261022-eval-dekois-builtin-protenix-ranking; hitdisc-20261022-eval-dekois-builtin-quoted-carsidock-dekois; hitdisc-20261022-eval-dekois-builtin-quoted-glide-sp-dekois; hitdisc-20261022-eval-dekois-builtin-quoted-gold-chemplp-dekois; hitdisc-20261022-eval-dekois-builtin-quoted-karmadock-aligned-dekois; hitdisc-20261022-eval-dekois-builtin-quoted-ledock-dekois; hitdisc-20261022-eval-dekois-builtin-quoted-surfdock-dekois; hitdisc-20261022-eval-dekois-builtin-quoted-surflex-dock-dekois; hitdisc-20261022-eval-dekois-builtin-quoted-tankbind-dekois
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