BindCraft Supplementary Data 1 does not let the per-target hit counts be recomputed
Supplementary data reconciliation of BindCraft
Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv) has 211 design rows across 13 target labels. Rows with a non-empty Binding cell, and the count of Binding = 1, against the prose: BBF-14 11 and 6 against 11 tested and 6 binding; Bet v1 7 and 2 against 7 and 2; CD45 16 and 4 against 16 and 4; Der f7 10 and 4 against 10 and 4; Der f21 7 and 4 against 7 and 4; IFNAR2 9 and 3 against 9 and 3; PD-1 53 and 13 against 53 and 13; SpCas9 6 and 6 against 6 and 6; CLDN1 7 and 6 against 7 and 6; PD-L1 13 and 11 against 9 tested and 7 binding; CrSAS-6 10 and 3 against 9 tested with no numerator in the prose; CbAgo 2 and 2 against 12 tested with no numerator in the prose. HER2 has 1 non-empty row and belongs to the AAV application. The three mismatches mean the filter the figure's aggregation implies cannot be applied to these rows, so under docs/collection.md the per-target counts for PD-L1, CrSAS-6 and CbAgo are recorded as a gap rather than computed.
Supplementary Data 1 holds one row per tested design with a Binding column of 1, 0 or an empty cell. Treating the non-empty cells as the tested set reconciles with the Results prose for nine of twelve targets and not for PD-L1, CrSAS-6 or CbAgo, so the row filter is ambiguous and no value is computed from these rows.
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 supplementary_data_reconciliation Context-only references | One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Fig. 1b caption; Results prose Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field supplementary_data_reconciliation Context-only references | BindCraft Supplementary Information and Supplementary Data 1 (Pacesa et al., Nature 2025) Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Fig. 1b caption; Results prose Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary files archive for PMC12507698, holding 41586_2025_9429_MOESM1_ESM.pdf (Supplementary Text, Figs. 1-6, Table 1 and References) and 41586_2025_9429_MOESM4_ESM.csv (Supplementary Data 1) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the whole supplementary archive. Member hashes: Supplementary Information PDF and Supplementary Data 1 CSV were read from this archive without re-download. |
| Source location Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Fig. 1b caption; Results prose Context-only references | One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Fig. 1b caption; Results prose Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Source location Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Fig. 1b caption; Results prose Context-only references | BindCraft Supplementary Information and Supplementary Data 1 (Pacesa et al., Nature 2025) Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Fig. 1b caption; Results prose Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary files archive for PMC12507698, holding 41586_2025_9429_MOESM1_ESM.pdf (Supplementary Text, Figs. 1-6, Table 1 and References) and 41586_2025_9429_MOESM4_ESM.csv (Supplementary Data 1) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the whole supplementary archive. Member hashes: Supplementary Information PDF and Supplementary Data 1 CSV were read from this archive without re-download. |
| Claimed value Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv) has 211 design rows across 13 target labels. Rows with a non-empty Binding cell, and the count of Binding = 1, against the prose: BBF-14 11 and 6 against 11 tested and 6 binding; Bet v1 7 and 2 against 7 and 2; CD45 16 and 4 against 16 and 4; Der f7 10 and 4 against 10 and 4; Der f21 7 and 4 against 7 and 4; IFNAR2 9 and 3 against 9 and 3; PD-1 53 and 13 against 53 and 13; SpCas9 6 and 6 against 6 and 6; CLDN1 7 and 6 against 7 and 6; PD-L1 13 and 11 against 9 tested and 7 binding; CrSAS-6 10 and 3 against 9 tested with no numerator in the prose; CbAgo 2 and 2 against 12 tested with no numerator in the prose. HER2 has 1 non-empty row and belongs to the AAV application. The three mismatches mean the filter the figure's aggregation implies cannot be applied to these rows, so under docs/collection.md the per-target counts for PD-L1, CrSAS-6 and CbAgo are recorded as a gap rather than computed. Context-only references | One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Fig. 1b caption; Results prose Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed value Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv) has 211 design rows across 13 target labels. Rows with a non-empty Binding cell, and the count of Binding = 1, against the prose: BBF-14 11 and 6 against 11 tested and 6 binding; Bet v1 7 and 2 against 7 and 2; CD45 16 and 4 against 16 and 4; Der f7 10 and 4 against 10 and 4; Der f21 7 and 4 against 7 and 4; IFNAR2 9 and 3 against 9 and 3; PD-1 53 and 13 against 53 and 13; SpCas9 6 and 6 against 6 and 6; CLDN1 7 and 6 against 7 and 6; PD-L1 13 and 11 against 9 tested and 7 binding; CrSAS-6 10 and 3 against 9 tested with no numerator in the prose; CbAgo 2 and 2 against 12 tested with no numerator in the prose. HER2 has 1 non-empty row and belongs to the AAV application. The three mismatches mean the filter the figure's aggregation implies cannot be applied to these rows, so under docs/collection.md the per-target counts for PD-L1, CrSAS-6 and CbAgo are recorded as a gap rather than computed. Context-only references | BindCraft Supplementary Information and Supplementary Data 1 (Pacesa et al., Nature 2025) Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Fig. 1b caption; Results prose Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary files archive for PMC12507698, holding 41586_2025_9429_MOESM1_ESM.pdf (Supplementary Text, Figs. 1-6, Table 1 and References) and 41586_2025_9429_MOESM4_ESM.csv (Supplementary Data 1) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the whole supplementary archive. Member hashes: Supplementary Information PDF and Supplementary Data 1 CSV were read from this archive without re-download. |
| Description Supplementary Data 1 holds one row per tested design with a Binding column of 1, 0 or an empty cell. Treating the non-empty cells as the tested set reconciles with the Results prose for nine of twelve targets and not for PD-L1, CrSAS-6 or CbAgo, so the row filter is ambiguous and no value is computed from these rows. Context-only references | One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Fig. 1b caption; Results prose Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Description Supplementary Data 1 holds one row per tested design with a Binding column of 1, 0 or an empty cell. Treating the non-empty cells as the tested set reconciles with the Results prose for nine of twelve targets and not for PD-L1, CrSAS-6 or CbAgo, so the row filter is ambiguous and no value is computed from these rows. Context-only references | BindCraft Supplementary Information and Supplementary Data 1 (Pacesa et al., Nature 2025) Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Fig. 1b caption; Results prose Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary files archive for PMC12507698, holding 41586_2025_9429_MOESM1_ESM.pdf (Supplementary Text, Figs. 1-6, Table 1 and References) and 41586_2025_9429_MOESM4_ESM.csv (Supplementary Data 1) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the whole supplementary archive. Member hashes: Supplementary Information PDF and Supplementary Data 1 CSV were read from this archive without re-download. |
| Relationship: subject uc-binder-20261022-pipeline-bindcraft Context-only references | One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Fig. 1b caption; Results prose Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Relationship: subject uc-binder-20261022-pipeline-bindcraft Context-only references | BindCraft Supplementary Information and Supplementary Data 1 (Pacesa et al., Nature 2025) Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Fig. 1b caption; Results prose Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary files archive for PMC12507698, holding 41586_2025_9429_MOESM1_ESM.pdf (Supplementary Text, Figs. 1-6, Table 1 and References) and 41586_2025_9429_MOESM4_ESM.csv (Supplementary Data 1) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the whole supplementary archive. Member hashes: Supplementary Information PDF and Supplementary Data 1 CSV were read from this archive without re-download. |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- BindCraft Supplementary Information and Supplementary Data 1 (Pacesa et al., Nature 2025) · Original source · Supplementary files archive for PMC12507698, holding 41586_2025_9429_MOESM1_ESM.pdf (Supplementary Text, Figs. 1-6, Table 1 and References) and 41586_2025_9429_MOESM4_ESM.csv (Supplementary Data 1)
- One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Original source · Nature, version of record; Europe PMC JATS full text for PMC12507698
Technical metadata and extraction receipts
Stable ID: uc-binder-20261022-claim-bindcraft-supplementary-data-1-ambiguous-filter
- field
- supplementary_data_reconciliation
- review
- artifact sha256: a402ac50b4860e24430494cb4344c569bf29ef3b8e769372adcd3298659267de; method: source-hash-verification; independent-cell-check; ai-assisted-source-review; method note: Re-downloaded from Europe PMC. The archive is generated per request: the byte count matched (13,409,376) but the SHA-256 did not, so the pinned archive hash does not identify a reproducible artifact. Checked at member level instead: 41586_2025_9429_MOESM1_ESM.pdf is faf09b8749f1d1785ab46beb917ad4d44b122904e4678c3a748f8dd4a600b2cd and 41586_2025_9429_MOESM4_ESM.csv is c87fd6cd0a54fe57d840938be07449394abbd55318494c8cc0292b6417c16b4f. Supplementary Table 1 read from the PDF text layer and Supplementary Data 1 reparsed with an independent script.; note: Reviewed in docs/reviews/use-cases/binder-2026-10-22.md. Automated AI review of the source transcription only; it is not human scientific review and nothing here was reproduced experimentally.; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12507698/supplementaryFiles; reviewed at: 2026-10-22T15:00:00Z; reviewer: claude; reviewer note: Claude review agent, independent of the extraction agent; no human review claimed
- source locator
- Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Fig. 1b caption; Results prose
- value
- Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv) has 211 design rows across 13 target labels. Rows with a non-empty Binding cell, and the count of Binding = 1, against the prose: BBF-14 11 and 6 against 11 tested and 6 binding; Bet v1 7 and 2 against 7 and 2; CD45 16 and 4 against 16 and 4; Der f7 10 and 4 against 10 and 4; Der f21 7 and 4 against 7 and 4; IFNAR2 9 and 3 against 9 and 3; PD-1 53 and 13 against 53 and 13; SpCas9 6 and 6 against 6 and 6; CLDN1 7 and 6 against 7 and 6; PD-L1 13 and 11 against 9 tested and 7 binding; CrSAS-6 10 and 3 against 9 tested with no numerator in the prose; CbAgo 2 and 2 against 12 tested with no numerator in the prose. HER2 has 1 non-empty row and belongs to the AAV application. The three mismatches mean the filter the figure's aggregation implies cannot be applied to these rows, so under docs/collection.md the per-target counts for PD-L1, CrSAS-6 and CbAgo are recorded as a gap rather than computed.
Related records
- subject: BindCraft