Most BindCraft targets were designed against a predicted structure, not a deposited complex
Target input provenance of BindCraft 12-target benchmark set
Supplementary Table 1, input structures as printed: PD-1 'AF2 prediction, trimmed to 32-146'; PD-L1 'AF2 prediction, trimmed to 18-132'; IFNAR2 '2LAG15, trimmed to 8-110'; CD45 'AF2 prediction of 5FMV16, split by extracellular fibronectin domains'; Claudin1 'AF2 prediction of CLN1-147'; BBF-14 '9HAG7'; CrSAS-6 'AF2 prediction, trimmed to 15-160'; Der f7 'AF2 prediction with 3UV1 template17'; Der f21 'AF2 dimer prediction with 5YNY template18, trimmed to 25-136'; Bet v1 'AF2 prediction'; SpCas9 'AF2 prediction with 4ZT0 template, trimmed to 96-174 + 306-446'; CbAgo 'AF2 prediction with 6QZK template20, trimmed to 1-175 + 298-343 + 635-689 (N+PIWI) or 180-276 (PAZ)'; HER2 (AAV) '1N8Z21, trimmed to 23-268'; PD-L1 (AAV) 'AF2 prediction, trimmed to 18-132'. Superscript reference markers are glued to the accessions in the PDF text layer and are transcribed as printed.
Supplementary Table 1 shows that nine of the twelve benchmark targets were designed against an AlphaFold2 prediction, in four cases with a PDB template, and three against a deposited structure. None of the inputs is a solved complex with a known binder, so the target inputs do not carry a known binding partner.
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.
6 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field target_input_provenance Context-only references | BindCraft Supplementary Information and Supplementary Data 1 (Pacesa et al., Nature 2025) Supplementary Table 1, column 'Input PDB' 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 Table 1, column 'Input PDB' Context-only references | BindCraft Supplementary Information and Supplementary Data 1 (Pacesa et al., Nature 2025) Supplementary Table 1, column 'Input PDB' 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 Table 1, input structures as printed: PD-1 'AF2 prediction, trimmed to 32-146'; PD-L1 'AF2 prediction, trimmed to 18-132'; IFNAR2 '2LAG15, trimmed to 8-110'; CD45 'AF2 prediction of 5FMV16, split by extracellular fibronectin domains'; Claudin1 'AF2 prediction of CLN1-147'; BBF-14 '9HAG7'; CrSAS-6 'AF2 prediction, trimmed to 15-160'; Der f7 'AF2 prediction with 3UV1 template17'; Der f21 'AF2 dimer prediction with 5YNY template18, trimmed to 25-136'; Bet v1 'AF2 prediction'; SpCas9 'AF2 prediction with 4ZT0 template, trimmed to 96-174 + 306-446'; CbAgo 'AF2 prediction with 6QZK template20, trimmed to 1-175 + 298-343 + 635-689 (N+PIWI) or 180-276 (PAZ)'; HER2 (AAV) '1N8Z21, trimmed to 23-268'; PD-L1 (AAV) 'AF2 prediction, trimmed to 18-132'. Superscript reference markers are glued to the accessions in the PDF text layer and are transcribed as printed. Context-only references | BindCraft Supplementary Information and Supplementary Data 1 (Pacesa et al., Nature 2025) Supplementary Table 1, column 'Input PDB' 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 Table 1 shows that nine of the twelve benchmark targets were designed against an AlphaFold2 prediction, in four cases with a PDB template, and three against a deposited structure. None of the inputs is a solved complex with a known binder, so the target inputs do not carry a known binding partner. Context-only references | BindCraft Supplementary Information and Supplementary Data 1 (Pacesa et al., Nature 2025) Supplementary Table 1, column 'Input PDB' 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-data-bindcraft-twelve-benchmark-targets Context-only references | BindCraft Supplementary Information and Supplementary Data 1 (Pacesa et al., Nature 2025) Supplementary Table 1, column 'Input PDB' 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. |
| Name Most BindCraft targets were designed against a predicted structure, not a deposited complex Context-only references | BindCraft Supplementary Information and Supplementary Data 1 (Pacesa et al., Nature 2025) Supplementary Table 1, column 'Input PDB' 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
1 source record 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)
Technical metadata and extraction receipts
Stable ID: uc-binder-20261022-claim-bindcraft-target-input-provenance
- field
- target_input_provenance
- 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 Table 1, column 'Input PDB'
- value
- Supplementary Table 1, input structures as printed: PD-1 'AF2 prediction, trimmed to 32-146'; PD-L1 'AF2 prediction, trimmed to 18-132'; IFNAR2 '2LAG15, trimmed to 8-110'; CD45 'AF2 prediction of 5FMV16, split by extracellular fibronectin domains'; Claudin1 'AF2 prediction of CLN1-147'; BBF-14 '9HAG7'; CrSAS-6 'AF2 prediction, trimmed to 15-160'; Der f7 'AF2 prediction with 3UV1 template17'; Der f21 'AF2 dimer prediction with 5YNY template18, trimmed to 25-136'; Bet v1 'AF2 prediction'; SpCas9 'AF2 prediction with 4ZT0 template, trimmed to 96-174 + 306-446'; CbAgo 'AF2 prediction with 6QZK template20, trimmed to 1-175 + 298-343 + 635-689 (N+PIWI) or 180-276 (PAZ)'; HER2 (AAV) '1N8Z21, trimmed to 23-268'; PD-L1 (AAV) 'AF2 prediction, trimmed to 18-132'. Superscript reference markers are glued to the accessions in the PDF text layer and are transcribed as printed.
Related records
- subject: BindCraft 12-target benchmark set