DUD-E (Directory of Useful Decoys, Enhanced)
Virtual-screening benchmark that scores ligand enrichment against property-matched decoys for each target.
No reviewed evaluations are linked here in this release. See the sources below.
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.
Published results still to collect
This release has no source-checked evaluations linked to this page. It does not mean that the benchmark has no published results.
Charts will appear when compatible result tables have been checked against their sources.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Additional methodological details, tasks and evaluated configurations have not yet been extracted into a structured profile for this benchmark. Consult the linked sources and evaluation records below.
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.
No concrete protocols are explicitly linked to this suite. Protocol identification and baseline selection are outstanding.
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-11-02-a7f03c9e55a5. 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.
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 2026-11-02-a7f03c9e55a5 · Record review: discovered
2 source records and release history
- Mysinger et al. 2012, J Med Chem 55:6582 (DUD-E, Europe PMC full text) · Original source · PMC3405771 (J Med Chem 2012)
- Chen et al. 2019, PLoS ONE 14:e0220113 (hidden bias in DUD-E, Europe PMC full text) · Original source · PMC6701836 (PLoS ONE 2019)
Technical metadata and extraction receipts
Stable ID: hitdisc-20261022-benchmark-dude
- areas
- molecular-interactions
- contexts
- research
- entity level
- suite
- task
- Protein-ligand virtual screening (library ranking)
- version
- DUD-E as published in 2012; no release identifier is printed in the abstract
- scope note
- 102 proteins with 22886 clustered ligands drawn from ChEMBL, each ligand with 50 property-matched decoys drawn to be topologically dissimilar to the ligands. Targets include GPCRs and ion channels.
- source locator
- Abstract
- limitations
- Chen et al. 2019 report that convolutional neural network models trained on DUD-E can distinguish actives from decoys using artefacts of how the decoys were constructed rather than protein-ligand binding, so DUD-E performance of such models is misleading.; Registered without results: no evaluation on DUD-E is extracted in this batch.
- 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: 8f20c3adec704671ea668742622567a7c6aec9b38f6d804f977c175209fa500d; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3405771/fullTextXML; receipt: data/omics/use-case-coverage-hitdisc-20261022/review.json