Evidence claim

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

Use case: Find hits for a target by virtual screening
Assessed by: DEKOIS 2.0 screening by rescoring Protenix-predicted complexes (Shen et al. 2025 Table 2, Protenix block)
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.

13 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-rescore-protenix: 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-rescore-protenix: 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-rescore-protenix: 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-rescore-protenix: 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-rescore-protenix: 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-rescore-protenix Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-dekois-rescore-protenix: 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-rescore-protenix: 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 3 values Structures the Protein Preparation Wizard could not process were given an extremely low score rather than excluded. 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-rescore-protenix: 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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hitdisc-20261022-result-dekois-rescore-protenix-rescore-rtmscore-on-protenix-poses-enrichment-factor-ef5pct-med fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 71fbcd70e6fd813a5e0ca1d7aa6ec498924ab66673e6e0a5ab3de6e08a26e2da record id hitdisc-20261022-source-shen2025 fields status attributes.artifact_sha256 sha256 f94ba0aaa2aea1b6a65dae4fbc3549071ccac4eeba75390ada5a10f6b5ccd823 record id use-case-hit-discovery-virtual-screening fields status name description facets attributes.question attributes.decision attributes.inputs attributes.output attributes.exclusions attributes.setting attributes.clinical_scope attributes.intended_users sha256 dc57177bbc7bd26bcb01b194ecc3598e987ff5dc02a07432c4585abfde8e97cc Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-dekois-rescore-protenix: 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, for the same reason as the built-in-score arm: right endpoint, synthetic negatives. This arm answers a narrower question that still bears on the decision, namely whether a classical or deep-learning scoring function applied to a co-folded pose beats the model's own confidence score. On Protenix poses only Gnina CNNscore (EF1% 16.69, mean) and RTMScore (20.37) approach the co-folding ipTM value (16.81), while Glide SP reaches 12.65. Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-dekois-rescore-protenix: 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

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)

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Technical metadata and extraction receipts

Stable ID: hitdisc-20261022-use-case-mapping-shen-dekois-rescore-protenix

field: links:assessed_by:hitdisc-20261022-protocol-shen-dekois-rescore-protenix
value: hitdisc-20261022-protocol-shen-dekois-rescore-protenix
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, for the same reason as the built-in-score arm: right endpoint, synthetic negatives. This arm answers a narrower question that still bears on the decision, namely whether a classical or deep-learning scoring function applied to a co-folded pose beats the model's own confidence score. On Protenix poses only Gnina CNNscore (EF1% 16.69, mean) and RTMScore (20.37) approach the co-folding ipTM value (16.81), while Glide SP reaches 12.65.
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: Structures the Protein Preparation Wizard could not process were given an extremely low score rather than excluded.; 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-rescore-protenix: 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, rescoring of Protenix-predicted complexes (13 arms)
stratum order: 2
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-rescore-protenix-protenix-iptm; hitdisc-20261022-eval-dekois-rescore-protenix-rescore-glide-sp-on-protenix-poses; hitdisc-20261022-eval-dekois-rescore-protenix-rescore-glide-xp-on-protenix-poses; hitdisc-20261022-eval-dekois-rescore-protenix-rescore-gnina-ad4-on-protenix-poses; hitdisc-20261022-eval-dekois-rescore-protenix-rescore-gnina-cnnaffinity-on-protenix-poses; hitdisc-20261022-eval-dekois-rescore-protenix-rescore-gnina-cnnscore-on-protenix-poses; hitdisc-20261022-eval-dekois-rescore-protenix-rescore-gnina-vina-on-protenix-poses; hitdisc-20261022-eval-dekois-rescore-protenix-rescore-gnina-vinardo-on-protenix-poses; hitdisc-20261022-eval-dekois-rescore-protenix-rescore-igmodel-pkd-on-protenix-poses; hitdisc-20261022-eval-dekois-rescore-protenix-rescore-igmodel-rmsd-on-protenix-poses; hitdisc-20261022-eval-dekois-rescore-protenix-rescore-pignet2-on-protenix-poses; hitdisc-20261022-eval-dekois-rescore-protenix-rescore-planet-on-protenix-poses; hitdisc-20261022-eval-dekois-rescore-protenix-rescore-rtmscore-on-protenix-poses
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subject: Find hits for a target by virtual screening

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