Evidence claim
Summary of the evidence for use-case-hit-discovery-virtual-screening
Summary of Find hits for a target by virtual screening
Three sources in this store score machine-learning and co-folding methods against docking on the same screening data, and what the numbers say depends on how the negatives were built. On DEKOIS 2.0, whose 79 targets each pair 40 validated actives with 1,200 property-matched decoys selected from ZINC (1:30), the co-folding confidence scores enrich strongly and beat the docking arms. AF3 min-iPAE gives a mean EF1% of 23.15 and Boltz-2 min-iPAE 22.73, against 12.01 for the Glide SP row quoted from another paper, 5.16 for Gnina Vina and 2.94 for TankBind; the best rescoring of a co-folded pose, RTMScore on AF3 poses, reaches 21.34. The authors flag their own Boltz-2 affinity arms (mean EF1% 23.54 and 25.84) as likely over-estimates because Boltz-2 drew affinity data from the same public databases that source DEKOIS 2.0. On GPCRrecent, 16 targets whose first crystal structures were released after 2022 with decoys generated by a conditional recurrent neural network at 1:50, every value falls and the margin narrows: Boltz-2 min-iPAE gives a mean EF1% of 13.96 against 5.02 for Glide SP and 3.65 for Gnina Vina. On the five LIT-PCBA targets where the inactives were experimentally measured, the margin largely disappears: averaged over the five targets Boltz-2 min-iPAE gives EF1% 9.30 and NEF1% 0.100 against Glide SP's 6.79 and 0.079, and on TP53 both Boltz-2 scores give EF1% 0.00 while Protenix ipTM gives 5.00 and Glide SP 3.75. A separate audit of LIT-PCBA reports 323 active training-validation analogue pairs at ECFP4 Tanimoto at or above 0.6 in ALDH1 alone and 2,491 2D-identical inactives shared between training and validation across targets, and concludes that a parameter-free memorisation baseline matches or exceeds published deep-learning results there, so every LIT-PCBA value above carries that limit. Where the negatives are compounds a docking screen already ranked highly and every compound was synthesised and assayed, the ordering changes. On the AmpC list (247 inhibitors among 1,293 tested compounds from a 1.7-billion molecule screen) DOCK3.7 separates binders best, AUC 76.5, against 68.1 for Boltz-2 pIC50 and 60.5 for AF3 L-pLDDT. On the dopamine D4 list (205 binders among 541) docking and Boltz-2 are indistinguishable at the precision printed (both about 71) and AF3 L-pLDDT is worse than random at 46.4. Only on the sigma-2 list (201 binders among 506) does a co-folding score lead, Boltz-2 pIC50 at 83.8 against DOCK3.7's 78.8, with AF3 L-pLDDT at 56.1. In the one blinded prospective challenge, CACHE #3 on the SARS-CoV-2 Nsp3 macrodomain, 23 workflows selected 1,739 compounds that were synthesised and assayed; 28 advanced to hit expansion and 29 confirmed hits scored above 15, four of them judged chemically novel. Twelve of the 23 workflows returned no confirmed hit from their own selection of 41 to 99 compounds. When every workflow was applied to the same merged 1,739-compound library, WF1696, which the article describes as a purely physics-based method, captured 2 of the 4 Tier 1 and 9 of the 25 Tier 2 confirmed hits from 99 predicted actives, which the authors report as did better than any other method in retrieving hits from the collection of all molecules selected in Round 1. Cost bounds all of this: co-folding one protein-ligand pair takes 7.79 to 34.58 seconds per compound on one NVIDIA H100 with pre-computed MSAs, which is why the LIT-PCBA arm covers five targets rather than fifteen. No docking tool was timed on the same hardware, no ligand-similarity or pharmacophore baseline is scored anywhere in this batch, and no result here estimates the hit rate of an untested library.
Draft summary of what the extracted evidence shows. Descriptive only, not reviewed.
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.
40 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Citation locations5 values
| Herasymenko et al. 2026, J Chem Inf Model (CACHE Challenge #3, Europe PMC full text) Shen et al. 2025 Tables 1-5; Kim, Correy, Hall et al. 2026 Results; Herasymenko et al. 2026 Results and sheet S8; arXiv:2507.21404v2 Abstract 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) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Citation locations5 values
| Herasymenko et al. 2026, CACHE Challenge #3, Supporting Information workbook ci5c02441_si_002.xlsx Shen et al. 2025 Tables 1-5; Kim, Correy, Hall et al. 2026 Results; Herasymenko et al. 2026 Results and sheet S8; arXiv:2507.21404v2 Abstract 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 | not individually reviewed No individual claim review recorded Audit detailsField: 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 |
Citation locations5 values
| Kim, Correy, Hall et al. 2026, eLife 15:RP110475 (Europe PMC full text) Shen et al. 2025 Tables 1-5; Kim, Correy, Hall et al. 2026 Results; Herasymenko et al. 2026 Results and sheet S8; arXiv:2507.21404v2 Abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC13657626 (eLife 2026;15:RP110475, version of record published 2026-10-12) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Citation locations5 values
| Huang, Knight and Naprienko 2025, arXiv:2507.21404v2 (abstract page) Shen et al. 2025 Tables 1-5; Kim, Correy, Hall et al. 2026 Results; Herasymenko et al. 2026 Results and sheet S8; arXiv:2507.21404v2 Abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv:2507.21404v2, submitted 2025-07-29, this version 2025-08-07 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: This is a mutable web page: artifact_sha256 describes the single retrieval of 2026-10-22T11:59:20Z and a later change to the page would change it. |
Citation locations5 values
| Shen et al. 2025, Chemical Science (Europe PMC full text) Shen et al. 2025 Tables 1-5; Kim, Correy, Hall et al. 2026 Results; Herasymenko et al. 2026 Results and sheet S8; arXiv:2507.21404v2 Abstract 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 field summary Context-only references | Herasymenko et al. 2026, J Chem Inf Model (CACHE Challenge #3, Europe PMC full text) Shen et al. 2025 Tables 1-5; Kim, Correy, Hall et al. 2026 Results; Herasymenko et al. 2026 Results and sheet S8; arXiv:2507.21404v2 Abstract 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) | 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 field summary Context-only references | Herasymenko et al. 2026, CACHE Challenge #3, Supporting Information workbook ci5c02441_si_002.xlsx Shen et al. 2025 Tables 1-5; Kim, Correy, Hall et al. 2026 Results; Herasymenko et al. 2026 Results and sheet S8; arXiv:2507.21404v2 Abstract 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 | not individually reviewed No individual claim review recorded Audit detailsField: 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 |
| Claimed field summary Context-only references | Kim, Correy, Hall et al. 2026, eLife 15:RP110475 (Europe PMC full text) Shen et al. 2025 Tables 1-5; Kim, Correy, Hall et al. 2026 Results; Herasymenko et al. 2026 Results and sheet S8; arXiv:2507.21404v2 Abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC13657626 (eLife 2026;15:RP110475, version of record published 2026-10-12) | 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 field summary Context-only references | Huang, Knight and Naprienko 2025, arXiv:2507.21404v2 (abstract page) Shen et al. 2025 Tables 1-5; Kim, Correy, Hall et al. 2026 Results; Herasymenko et al. 2026 Results and sheet S8; arXiv:2507.21404v2 Abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv:2507.21404v2, submitted 2025-07-29, this version 2025-08-07 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: This is a mutable web page: artifact_sha256 describes the single retrieval of 2026-10-22T11:59:20Z and a later change to the page would change it. |
| Claimed field summary Context-only references | Shen et al. 2025, Chemical Science (Europe PMC full text) Shen et al. 2025 Tables 1-5; Kim, Correy, Hall et al. 2026 Results; Herasymenko et al. 2026 Results and sheet S8; arXiv:2507.21404v2 Abstract 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
5 source records and release history
- Shen et al. 2025, Chemical Science (Europe PMC full text) · Original source · PMC12704515 (Chem Sci, published 2025-12-11)
- Kim, Correy, Hall et al. 2026, eLife 15:RP110475 (Europe PMC full text) · Original source · PMC13657626 (eLife 2026;15:RP110475, version of record published 2026-10-12)
- Herasymenko et al. 2026, J Chem Inf Model (CACHE Challenge #3, Europe PMC full text) · Original source · PMC12892310 (J Chem Inf Model, published 2026-01-21)
- 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
- Huang, Knight and Naprienko 2025, arXiv:2507.21404v2 (abstract page) · Original source · arXiv:2507.21404v2, submitted 2025-07-29, this version 2025-08-07
Technical metadata and extraction receipts
Stable ID: hitdisc-20261022-use-case-summary
- field
- summary
- value
- Three sources in this store score machine-learning and co-folding methods against docking on the same screening data, and what the numbers say depends on how the negatives were built. On DEKOIS 2.0, whose 79 targets each pair 40 validated actives with 1,200 property-matched decoys selected from ZINC (1:30), the co-folding confidence scores enrich strongly and beat the docking arms. AF3 min-iPAE gives a mean EF1% of 23.15 and Boltz-2 min-iPAE 22.73, against 12.01 for the Glide SP row quoted from another paper, 5.16 for Gnina Vina and 2.94 for TankBind; the best rescoring of a co-folded pose, RTMScore on AF3 poses, reaches 21.34. The authors flag their own Boltz-2 affinity arms (mean EF1% 23.54 and 25.84) as likely over-estimates because Boltz-2 drew affinity data from the same public databases that source DEKOIS 2.0. On GPCRrecent, 16 targets whose first crystal structures were released after 2022 with decoys generated by a conditional recurrent neural network at 1:50, every value falls and the margin narrows: Boltz-2 min-iPAE gives a mean EF1% of 13.96 against 5.02 for Glide SP and 3.65 for Gnina Vina. On the five LIT-PCBA targets where the inactives were experimentally measured, the margin largely disappears: averaged over the five targets Boltz-2 min-iPAE gives EF1% 9.30 and NEF1% 0.100 against Glide SP's 6.79 and 0.079, and on TP53 both Boltz-2 scores give EF1% 0.00 while Protenix ipTM gives 5.00 and Glide SP 3.75. A separate audit of LIT-PCBA reports 323 active training-validation analogue pairs at ECFP4 Tanimoto at or above 0.6 in ALDH1 alone and 2,491 2D-identical inactives shared between training and validation across targets, and concludes that a parameter-free memorisation baseline matches or exceeds published deep-learning results there, so every LIT-PCBA value above carries that limit. Where the negatives are compounds a docking screen already ranked highly and every compound was synthesised and assayed, the ordering changes. On the AmpC list (247 inhibitors among 1,293 tested compounds from a 1.7-billion molecule screen) DOCK3.7 separates binders best, AUC 76.5, against 68.1 for Boltz-2 pIC50 and 60.5 for AF3 L-pLDDT. On the dopamine D4 list (205 binders among 541) docking and Boltz-2 are indistinguishable at the precision printed (both about 71) and AF3 L-pLDDT is worse than random at 46.4. Only on the sigma-2 list (201 binders among 506) does a co-folding score lead, Boltz-2 pIC50 at 83.8 against DOCK3.7's 78.8, with AF3 L-pLDDT at 56.1. In the one blinded prospective challenge, CACHE #3 on the SARS-CoV-2 Nsp3 macrodomain, 23 workflows selected 1,739 compounds that were synthesised and assayed; 28 advanced to hit expansion and 29 confirmed hits scored above 15, four of them judged chemically novel. Twelve of the 23 workflows returned no confirmed hit from their own selection of 41 to 99 compounds. When every workflow was applied to the same merged 1,739-compound library, WF1696, which the article describes as a purely physics-based method, captured 2 of the 4 Tier 1 and 9 of the 25 Tier 2 confirmed hits from 99 predicted actives, which the authors report as did better than any other method in retrieving hits from the collection of all molecules selected in Round 1. Cost bounds all of this: co-folding one protein-ligand pair takes 7.79 to 34.58 seconds per compound on one NVIDIA H100 with pre-computed MSAs, which is why the LIT-PCBA arm covers five targets rather than fifteen. No docking tool was timed on the same hardware, no ligand-similarity or pharmacophore baseline is scored anywhere in this batch, and no result here estimates the hit rate of an untested library.
- source locator
- Shen et al. 2025 Tables 1-5; Kim, Correy, Hall et al. 2026 Results; Herasymenko et al. 2026 Results and sheet S8; arXiv:2507.21404v2 Abstract
- citation locators
- source id: hitdisc-20261022-source-shen2025; locator: Tables 1, 2, 3, 4 and 5; source id: hitdisc-20261022-source-kim2026; locator: Results 'Co-folding struggles to reliably re-rank docking hit lists'; source id: hitdisc-20261022-source-cache3; locator: Results 'Discovering Chemically Novel Ligands Was Challenging' and 'Trends and Strategies from the Best Performing Computational Workflows'; source id: hitdisc-20261022-source-cache3-si002; locator: Sheet 'S8'; source id: hitdisc-20261022-source-litpcba-audit; locator: Abstract
- reason
- Hit-discovery use-case pass 2026-10-22 (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
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