CACHE #3 merged Round 1 library prediction per workflow (Herasymenko et al. 2026 Table S8)
Have every CACHE #3 workflow predict which of the same 1739 Round 1 compounds are active, and count the confirmed Tier 1 and Tier 2 hits among each workflow's predicted actives.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
19 recorded evaluations, 171 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
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All evaluations
19 evaluations · 171 results. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- CACHE #3 workflow WF1687: merged library outcome
- CACHE #3 workflow WF1689: merged library outcome
- CACHE #3 workflow WF1690: merged library outcome
- CACHE #3 workflow WF1691: merged library outcome
- CACHE #3 workflow WF1696: merged library outcome
- CACHE #3 workflow WF1697: merged library outcome
- CACHE #3 workflow WF1700: merged library outcome
- CACHE #3 workflow WF1702: merged library outcome
- CACHE #3 workflow WF1704: merged library outcome
- CACHE #3 workflow WF1705: merged library outcome
- CACHE #3 workflow WF1706: merged library outcome
- CACHE #3 workflow WF1707: merged library outcome
Baseline coverage
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- Author-reported evaluations
- 19
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Proposed control: requires review
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Conventional reference
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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.
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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.
2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Metric qualifier confirmed hits among one workflow's predicted actives on the merged 1739-compound library Individual claims | Herasymenko et al. 2026, J Chem Inf Model (CACHE Challenge #3, Europe PMC full text) Sheet 'S8', columns R, S and T; the stored cell formulas in xl/worksheets/sheet9.xml Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12892310 (J Chem Inf Model, published 2026-01-21) | conflicting claim ["scope-review","independent-cell-check"] · 2026-10-22 Audit detailsCorrection found by the independent review pass of batch use-case-coverage-hitdisc-20261022. The previous value is kept here. Conflicting source claim: Field: Claim: metadata-correction-7eaef94c57753b967ce9 Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metric qualifier confirmed hits among one workflow's predicted actives on the merged 1739-compound library Individual claims | Herasymenko et al. 2026, CACHE Challenge #3, Supporting Information workbook ci5c02441_si_002.xlsx Sheet 'S8', columns R, S and T; the stored cell formulas in xl/worksheets/sheet9.xml Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: ci5c02441_si_002.xlsx, member of the Europe PMC supplementary archive of PMC12892310 | conflicting claim ["scope-review","independent-cell-check"] · 2026-10-22 Audit detailsCorrection found by the independent review pass of batch use-case-coverage-hitdisc-20261022. The previous value is kept here. Conflicting source claim: Field: Claim: metadata-correction-7eaef94c57753b967ce9 Source artifact SHA-256: Hash scope: artifact_sha256 is the SHA-256 of the member file ci5c02441_si_002.xlsx. The Europe PMC supplementaryFiles endpoint assembles a zip per request, so the archive's own hash is not stable; the member file's bytes are. The publisher's direct supplement URL (https://pubs.acs.org/doi/suppl/10.1021/acs.jcim.5c02441/suppl_file/ci5c02441_si_002.xlsx) returned HTTP 403 on 2026-10-22. Archive member: ci5c02441_si_002.xlsx |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- Herasymenko et al. 2026, CACHE Challenge #3, Supporting Information workbook ci5c02441_si_002.xlsx · Original source · ci5c02441_si_002.xlsx, member of the Europe PMC supplementary archive of PMC12892310
Technical metadata and extraction receipts
Stable ID: hitdisc-20261022-protocol-cache3-merged-library
- areas
- molecular-interactions
- contexts
- research
- task
- Protein-ligand virtual screening (library ranking)
- publication status
- peer_reviewed
- 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: 5e655da5728da46c6a57882c5fef0643c057536d7897d16b9c98f6d55c12f5fe; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12892310/supplementaryFiles; receipt: data/omics/use-case-coverage-hitdisc-20261022/review.json
- metric
- count
- metric direction
- higher
- unit
- count
- unit detail
- compounds
- metric qualifier
- confirmed hits among one workflow's predicted actives on the merged 1739-compound library
- metric definition
- Every workflow was applied to the merged library of all 1739 Round 1 compounds. Confirmed hits with a score above 15 were clustered into four chemically novel Tier 1 compounds and 25 Tier 2 compounds. Columns L to Q are counts. Columns R, S and T are stored as the formulas 1000*N/L, 1000*O/L and R+S, so they are confirmed Tier 1 or Tier 2 hits per 1000 compounds predicted active; the Figure 6c caption's wording, 'the aggregated score of all compounds predicted active divided by the number of compounds predicted to be actives', does not describe that formula.
- protocol
- Complementary evaluation scheme in which all computational workflows are applied to the same chemical library, so that selection of the library does not differ between them.
- denominator
- 1739
- version
- Herasymenko et al. 2026, Supporting Information table S8
- source locator
- Sheet 'S8' of ci5c02441_si_002.xlsx, merged-library columns; Figure 6 caption
- limitations
- The library is the union of what the 23 workflows themselves selected, so it is not an independent library and each workflow's own picks are in it.; Four of the 23 workflows (1694, 1695, 1716, 1717) have no values printed in these columns; they are recorded as absent, not as zero.; Only 29 confirmed hits scored above 15, four of them chemically novel, so the Tier 1 counts rest on four compounds in total.; The two normalised columns are labelled as counts of hits while the Figure 6c caption defines the normalised quantity as an aggregated score divided by the number of compounds predicted active. The stored cell formulas (1000*N/L and 1000*O/L) agree with the column labels and not with the caption. The sheet's final column has no printed header at all; its formula is R+S.; Columns L to Q are counts of compounds, not rates. Columns R, S and T are rates: the workbook stores them as 1000*N/L, 1000*O/L and R+S, so each is confirmed Tier 1 or Tier 2 hits per 1000 compounds predicted active. Predicting the merged library is also not the same task as selecting compounds to synthesise.; The article is internally inconsistent about Figure 6. The Results section 'Trends and Strategies from the Best Performing Computational Workflows' calls panels a, b and c 'top scoring compounds, top hit rates, and top selections from the merged Round 1 library', while the Figure 6 caption calls panel b 'the aggregated score of all Round 1 hits' and panel c the normalised Tier 1 and Tier 2 counts. The body text therefore calls an aggregated score a hit rate. No value in this batch is taken from Figure 6; every value is from sheet S8.
- scope note
- Prospective: predictions were submitted before any compound was synthesised or assayed.
Related records
- evaluates task: Protein–ligand virtual screening
- uses data: CACHE #3 Round 1 compound library
- part of: CACHE Challenge #3
- assessment: CACHE #3 workflow WF1687: merged library outcome
- assessment: CACHE #3 workflow WF1689: merged library outcome
- assessment: CACHE #3 workflow WF1690: merged library outcome
- assessment: CACHE #3 workflow WF1691: merged library outcome
- assessment: CACHE #3 workflow WF1696: merged library outcome
- assessment: CACHE #3 workflow WF1697: merged library outcome
- assessment: CACHE #3 workflow WF1700: merged library outcome
- assessment: CACHE #3 workflow WF1702: merged library outcome
- assessment: CACHE #3 workflow WF1704: merged library outcome
- assessment: CACHE #3 workflow WF1705: merged library outcome
- assessment: CACHE #3 workflow WF1706: merged library outcome
- assessment: CACHE #3 workflow WF1707: merged library outcome
- assessment: CACHE #3 workflow WF1708: merged library outcome
- assessment: CACHE #3 workflow WF1709: merged library outcome
- assessment: CACHE #3 workflow WF1712: merged library outcome
- assessment: CACHE #3 workflow WF1714: merged library outcome
- assessment: CACHE #3 workflow WF1715: merged library outcome
- assessment: CACHE #3 workflow WF1718: merged library outcome
- assessment: CACHE #3 workflow WF1879: merged library outcome
- subject: CACHE #3 merged-library protocol: normalised columns described by their stored formula
- subject: CACHE #3 normalised merged-library results: metric_qualifier corrected to the stored formula
- assessed by: Find hits for a target by virtual screening