Pipeline

BindCraft

Evidence concern: excluded from comparisons

Supplementary Data 1 has one row per tested design with a Binding column holding 1, 0 or an empty cell. Treating the non-empty cells as the tested set reproduces the prose counts for BBF-14 (11 tested, 6 binding), Bet v1 (7, 2), CD45 (16, 4), Der f7 (10, 4), Der f21 (7, 4), IFNAR2 (9, 3), PD-1 (53, 13), SpCas9 (6, 6) and CLDN1 (7, 6), but not for PD-L1 (13 non-empty rows with 11 binding against 9 tested with 7 binding in the prose), CrSAS-6 (10 non-empty rows against 9 tested) or CbAgo (2 non-empty rows against 12 tested). The row filter is therefore ambiguous and no value is computed from these rows.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; Results prose; Fig. 1b caption

Fig. 1b's caption defines success as binding observed on SPR, but the PD-1 screen was BLI in a bivalent Fc-fusion format and the CLDN1 screen used soluble analogues. The 46.3% average therefore pools targets measured under different endpoints.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Fig. 1b caption; Results 'Binders targeting cell-surface receptors' and 'Targeting unexplored binding sites'

BindCraft hallucinates a binder backbone and sequence by backpropagating through AlphaFold2 multimer, redesigns the binder core and surface with a solubility-weighted ProteinMPNN, and filters the designs on AlphaFold2 monomer and Rosetta scores.

Results are recorded on linked configurations and versions of this pipeline. Their settings and evaluations are kept separate below.

4 configurations with results

Results on linked records

This pipeline has no results of its own in this release. 4 linked records have results. They are not assigned to the underlying pipeline: each record keeps its own settings and evaluations, and its scores are on its own page.

Paired BindCraft designs joined by custom linkers with a GB1 solubility tag Configuration · configuration · 2 evaluations · 2 results
BindCraft default settings as entered in Adaptyv round 1 Configuration · configuration · 2 evaluations · 2 results
BindCraft with helical loss -2.0 as entered in Adaptyv round 2 Configuration · configuration · 2 evaluations · 2 results
BindCraft default settings Configuration · configuration · 23 evaluations · 24 results

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release history

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

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Technical metadata and extraction receipts

Stable ID: uc-binder-20261022-pipeline-bindcraft

areas: proteins-complexes; protein-structure
contexts: research
method types: specialist
access: Open pipeline; the paper describes an automated single workflow.
provenance note: Created from the BindCraft paper for the 2026-10-22 binder design pass.
reported name: BindCraft
review: artifact sha256: 74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d; method: source-hash-verification; independent-cell-check; ai-assisted-source-review; method note: Re-downloaded from Europe PMC (HTTP 200, 226,059 bytes) and the SHA-256 recomputed and matched. Own flattening of the JATS XML; every quoted locator sentence and every printed value checked verbatim against it by a parser written for this review.; 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/fullTextXML; 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: Fig. 1a; Results 'Accurate design of de novo binders'; Methods
version: As published in Nature 2025 (doi 10.1038/s41586-025-09429-6)

Related records

subject: Seven of the eight de novo binders in Adaptyv round 2 were designed with BindCraft
subject: BindCraft Supplementary Data 1 does not let the per-target hit counts be recomputed
configuration of: Paired BindCraft designs joined by custom linkers with a GB1 solubility tag
configuration of: BindCraft default settings as entered in Adaptyv round 1
configuration of: BindCraft with helical loss -2.0 as entered in Adaptyv round 2
configuration of: BindCraft default settings

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