Actives-to-decoys ratio and decoy construction differ by orders of magnitude between the screening benchmarks
Reported finding of DEKOIS 2.0
DEKOIS 2.0 holds 40 experimentally validated actives and 1200 property-matched decoys selected from ZINC per target, a ratio of 1:30. GPCRrecent holds BindingDB actives with decoys generated by a conditional recurrent neural network (TocoDecoy) at 1:50. LIT-PCBA's negatives are experimentally measured inactives, and its official per-target counts give ratios from 13 actives to 4,378 inactives (ESR_ago, about 1:337) and 88 to 3,820 (ESR_antago, about 1:43) up to 17 to 311,748 (ADRB2, about 1:18,000). DUD-E pairs each of 22,886 clustered ligands with 50 property-matched decoys. An enrichment factor is a ratio against random selection at a fixed fraction of the list, so it moves with both the ratio and the realism of the negatives; values from these benchmarks are not comparable with one another.
The composition facts that make raw enrichment factors incomparable between these benchmarks.
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.
12 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field reported_finding Context-only references | LIT-PCBA official project page, drugdesign.unistra.fr Shen et al. 2025 Methods 'Datasets' and 'Evaluation metrics'; LIT-PCBA official page data content table 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 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: 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. |
| Claimed field reported_finding Context-only references | Shen et al. 2025, Chemical Science (Europe PMC full text) Shen et al. 2025 Methods 'Datasets' and 'Evaluation metrics'; LIT-PCBA official page data content table Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12704515 (Chem Sci, published 2025-12-11) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Source location Shen et al. 2025 Methods 'Datasets' and 'Evaluation metrics'; LIT-PCBA official page data content table Context-only references | LIT-PCBA official project page, drugdesign.unistra.fr Shen et al. 2025 Methods 'Datasets' and 'Evaluation metrics'; LIT-PCBA official page data content table 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 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: 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. |
| Source location Shen et al. 2025 Methods 'Datasets' and 'Evaluation metrics'; LIT-PCBA official page data content table Context-only references | Shen et al. 2025, Chemical Science (Europe PMC full text) Shen et al. 2025 Methods 'Datasets' and 'Evaluation metrics'; LIT-PCBA official page data content table Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12704515 (Chem Sci, published 2025-12-11) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed value DEKOIS 2.0 holds 40 experimentally validated actives and 1200 property-matched decoys selected from ZINC per target, a ratio of 1:30. GPCRrecent holds BindingDB actives with decoys generated by a conditional recurrent neural network (TocoDecoy) at 1:50. LIT-PCBA's negatives are experimentally measured inactives, and its official per-target counts give ratios from 13 actives to 4,378 inactives (ESR_ago, about 1:337) and 88 to 3,820 (ESR_antago, about 1:43) up to 17 to 311,748 (ADRB2, about 1:18,000). DUD-E pairs each of 22,886 clustered ligands with 50 property-matched decoys. An enrichment factor is a ratio against random selection at a fixed fraction of the list, so it moves with both the ratio and the realism of the negatives; values from these benchmarks are not comparable with one another. Context-only references | LIT-PCBA official project page, drugdesign.unistra.fr Shen et al. 2025 Methods 'Datasets' and 'Evaluation metrics'; LIT-PCBA official page data content table 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 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: 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. |
| Claimed value DEKOIS 2.0 holds 40 experimentally validated actives and 1200 property-matched decoys selected from ZINC per target, a ratio of 1:30. GPCRrecent holds BindingDB actives with decoys generated by a conditional recurrent neural network (TocoDecoy) at 1:50. LIT-PCBA's negatives are experimentally measured inactives, and its official per-target counts give ratios from 13 actives to 4,378 inactives (ESR_ago, about 1:337) and 88 to 3,820 (ESR_antago, about 1:43) up to 17 to 311,748 (ADRB2, about 1:18,000). DUD-E pairs each of 22,886 clustered ligands with 50 property-matched decoys. An enrichment factor is a ratio against random selection at a fixed fraction of the list, so it moves with both the ratio and the realism of the negatives; values from these benchmarks are not comparable with one another. Context-only references | Shen et al. 2025, Chemical Science (Europe PMC full text) Shen et al. 2025 Methods 'Datasets' and 'Evaluation metrics'; LIT-PCBA official page data content table Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12704515 (Chem Sci, published 2025-12-11) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Description The composition facts that make raw enrichment factors incomparable between these benchmarks. Context-only references | LIT-PCBA official project page, drugdesign.unistra.fr Shen et al. 2025 Methods 'Datasets' and 'Evaluation metrics'; LIT-PCBA official page data content table 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 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: 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. |
| Description The composition facts that make raw enrichment factors incomparable between these benchmarks. Context-only references | Shen et al. 2025, Chemical Science (Europe PMC full text) Shen et al. 2025 Methods 'Datasets' and 'Evaluation metrics'; LIT-PCBA official page data content table Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12704515 (Chem Sci, published 2025-12-11) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Relationship: subject hitdisc-20261022-benchmark-dekois2 Context-only references | LIT-PCBA official project page, drugdesign.unistra.fr Shen et al. 2025 Methods 'Datasets' and 'Evaluation metrics'; LIT-PCBA official page data content table 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 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: 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. |
| Relationship: subject hitdisc-20261022-benchmark-dekois2 Context-only references | Shen et al. 2025, Chemical Science (Europe PMC full text) Shen et al. 2025 Methods 'Datasets' and 'Evaluation metrics'; LIT-PCBA official page data content table Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12704515 (Chem Sci, published 2025-12-11) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- Shen et al. 2025, Chemical Science (Europe PMC full text) · Original source · PMC12704515 (Chem Sci, published 2025-12-11)
- LIT-PCBA official project page, drugdesign.unistra.fr · Original source · Page as retrieved 2026-10-22; no version is printed on the page
Technical metadata and extraction receipts
Stable ID: hitdisc-20261022-claim-shen-decoy-ratios
- areas
- molecular-interactions
- contexts
- research
- field
- reported_finding
- value
- DEKOIS 2.0 holds 40 experimentally validated actives and 1200 property-matched decoys selected from ZINC per target, a ratio of 1:30. GPCRrecent holds BindingDB actives with decoys generated by a conditional recurrent neural network (TocoDecoy) at 1:50. LIT-PCBA's negatives are experimentally measured inactives, and its official per-target counts give ratios from 13 actives to 4,378 inactives (ESR_ago, about 1:337) and 88 to 3,820 (ESR_antago, about 1:43) up to 17 to 311,748 (ADRB2, about 1:18,000). DUD-E pairs each of 22,886 clustered ligands with 50 property-matched decoys. An enrichment factor is a ratio against random selection at a fixed fraction of the list, so it moves with both the ratio and the realism of the negatives; values from these benchmarks are not comparable with one another.
- source locator
- Shen et al. 2025 Methods 'Datasets' and 'Evaluation metrics'; LIT-PCBA official page data content table
- 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
Related records
- subject: DEKOIS 2.0