Per-series affinity-ranking values are not printed
Limitation of Public binding free energy benchmark (Ross et al. 2023)
Every value in Boltz-2 supplement Tables 11, 12 and 14 and in Ross et al. 2023 Table 3 is an average over series: the Boltz-2 metrics are computed per assay and averaged across assays weighted by compound count, and the Ross values are weighted averages over FEP graphs. Neither source prints a per-series value, and neither prints the spread across series, so these tables support statements about the mean over series and not about any one series.
What the extracted tables can and cannot support about ranking inside one series.
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 limitation Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Boltz-2 supplement appendix D.2.2 'Evaluation metrics' and Tables 11, 12, 14; Ross et al. 2023 Table 3 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Claimed field limitation Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Boltz-2 supplement appendix D.2.2 'Evaluation metrics' and Tables 11, 12, 14; Ross et al. 2023 Table 3 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | 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 Boltz-2 supplement appendix D.2.2 'Evaluation metrics' and Tables 11, 12, 14; Ross et al. 2023 Table 3 legend Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Boltz-2 supplement appendix D.2.2 'Evaluation metrics' and Tables 11, 12, 14; Ross et al. 2023 Table 3 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Source location Boltz-2 supplement appendix D.2.2 'Evaluation metrics' and Tables 11, 12, 14; Ross et al. 2023 Table 3 legend Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Boltz-2 supplement appendix D.2.2 'Evaluation metrics' and Tables 11, 12, 14; Ross et al. 2023 Table 3 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | 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 Every value in Boltz-2 supplement Tables 11, 12 and 14 and in Ross et al. 2023 Table 3 is an average over series: the Boltz-2 metrics are computed per assay and averaged across assays weighted by compound count, and the Ross values are weighted averages over FEP graphs. Neither source prints a per-series value, and neither prints the spread across series, so these tables support statements about the mean over series and not about any one series. Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Boltz-2 supplement appendix D.2.2 'Evaluation metrics' and Tables 11, 12, 14; Ross et al. 2023 Table 3 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Claimed value Every value in Boltz-2 supplement Tables 11, 12 and 14 and in Ross et al. 2023 Table 3 is an average over series: the Boltz-2 metrics are computed per assay and averaged across assays weighted by compound count, and the Ross values are weighted averages over FEP graphs. Neither source prints a per-series value, and neither prints the spread across series, so these tables support statements about the mean over series and not about any one series. Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Boltz-2 supplement appendix D.2.2 'Evaluation metrics' and Tables 11, 12, 14; Ross et al. 2023 Table 3 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | 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 What the extracted tables can and cannot support about ranking inside one series. Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Boltz-2 supplement appendix D.2.2 'Evaluation metrics' and Tables 11, 12, 14; Ross et al. 2023 Table 3 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Description What the extracted tables can and cannot support about ranking inside one series. Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Boltz-2 supplement appendix D.2.2 'Evaluation metrics' and Tables 11, 12, 14; Ross et al. 2023 Table 3 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | 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 uc-leadopt-20261022-benchmark-fep-public Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Boltz-2 supplement appendix D.2.2 'Evaluation metrics' and Tables 11, 12, 14; Ross et al. 2023 Table 3 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Relationship: subject uc-leadopt-20261022-benchmark-fep-public Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Boltz-2 supplement appendix D.2.2 'Evaluation metrics' and Tables 11, 12, 14; Ross et al. 2023 Table 3 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | 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
- Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Original source · bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344)
- The maximal and current accuracy of rigorous protein-ligand binding free energy calculations · Original source · Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784
Technical metadata and extraction receipts
Stable ID: uc-leadopt-20261022-claim-no-per-series-values
- field
- limitation
- value
- Every value in Boltz-2 supplement Tables 11, 12 and 14 and in Ross et al. 2023 Table 3 is an average over series: the Boltz-2 metrics are computed per assay and averaged across assays weighted by compound count, and the Ross values are weighted averages over FEP graphs. Neither source prints a per-series value, and neither prints the spread across series, so these tables support statements about the mean over series and not about any one series.
- source locator
- Boltz-2 supplement appendix D.2.2 'Evaluation metrics' and Tables 11, 12, 14; Ross et al. 2023 Table 3 legend
- review
- method: source-hash-verification; pdf-text-parse; independent-cell-check; rendered-source-visual-check; ai-assisted-source-review; method note: Re-retrieved all three sources and matched each pinned SHA-256. Re-rendered the Boltz-2 supplement with pdftotext -layout (poppler 26.08.0) and matched the text layer's recorded SHA-256. Re-read all 256 cells with a parser written for this review that does not import the extraction script, matching each result to its cell through its own source_locator, and separately read appendix tables 11, 12 and 14 from PNG renderings of PDF pages 29 and 30 at 160 dpi, and Ross Table 3 from the pinned XML markup. Checked printed value, numeric value, locator, metric concept, qualifier, direction, unit, uncertainty and the linked configuration, protocol and dataset, and that every N/A or '-' cell is recorded as missing with a reason.; reviewer: claude; reviewer note: Claude review agent, independent of the extraction agent; no human review claimed; reviewed at: 2026-10-22T13:40:00Z; artifact sha256: be867a5d92add8b223d47d882a4213ad489741f3e4d5081a0901a54370342569; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12262699/supplementaryFiles; note: Independent review 2026-10-22: the quoted wording was matched against the pinned artifact and the locator checked.