DEKOIS 2.0
Virtual-screening benchmark that scores a method on how well it ranks experimentally validated actives above property-matched decoys for each of its targets.
Results are recorded on the linked protocols, tasks or configurations listed below. Their settings and evaluations are kept separate.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Results on linked records
This benchmark has no results of its own in this release. 3 linked records have results. They are not assigned to the underlying benchmark: each record keeps its own settings and evaluations, and its scores are on its own page.
- DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Protocol · part of this benchmark · 24 evaluations · 240 results
- DEKOIS 2.0 screening by rescoring AF3-predicted complexes (Shen et al. 2025 Table 2, AF3 block) Protocol · part of this benchmark · 10 evaluations · 100 results
- DEKOIS 2.0 screening by rescoring Protenix-predicted complexes (Shen et al. 2025 Table 2, Protenix block) Protocol · part of this benchmark · 13 evaluations · 130 results
Methods and evaluation design
Procedure, tasks and evaluated configurations
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 6 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
Baseline status by linked protocol
- DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) · 0/2 roles measured
- DEKOIS 2.0 screening by rescoring AF3-predicted complexes (Shen et al. 2025 Table 2, AF3 block) · 0/2 roles measured
- DEKOIS 2.0 screening by rescoring Protenix-predicted complexes (Shen et al. 2025 Table 2, Protenix block) · 0/2 roles measured
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this benchmark. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Evidence
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Evidence table
Inspect claims, sources and review details
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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
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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)
Technical metadata and extraction receipts
Stable ID: hitdisc-20261022-benchmark-dekois2
- areas
- molecular-interactions
- contexts
- research
- entity level
- suite
- task
- Protein-ligand virtual screening (library ranking)
- scope note
- As described by Shen et al. 2025: 81 structurally diverse targets, each with 40 experimentally validated actives from BindingDB and 1200 property-matched decoys selected from ZINC, an actives-to-decoys ratio of 1:30. Data at http://www.dekois.com.
- source locator
- Methods 'Datasets'; Data availability
- limitations
- The decoys are synthetic property-matched molecules, not measured inactives, so enrichment factors on this benchmark are not comparable with benchmarks whose negatives were assayed.; The set was released over ten years before Shen et al. 2025 and its template protein structures may overlap substantially with the training data of the co-folding models scored on it (Results 'Performance on GPCRrecent dataset').
- missing metadata
- version: reason: unavailable; note: The DEKOIS 2.0 primary paper (doi 10.1021/ci400115b) is closed access and was not retrieved; the composition recorded here is as Shen et al. 2025 describe it
- 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: Record checked against the pinned source and the record contract. 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
Related records
- subject: Actives-to-decoys ratio and decoy construction differ by orders of magnitude between the screening benchmarks
- part of: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1)
- part of: DEKOIS 2.0 screening by rescoring AF3-predicted complexes (Shen et al. 2025 Table 2, AF3 block)
- part of: DEKOIS 2.0 screening by rescoring Protenix-predicted complexes (Shen et al. 2025 Table 2, Protenix block)