Result

Dissociation constant (binder2; apparent KD (Kd*) by BLI in a bivalent Fc-fusion format; the exact value could not be determined) of BindCraft default settings on BindCraft binder design target PD-1

lower than 1 nM Dissociation constant (binder2; apparent KD (Kd*) by BLI in a bivalent Fc-fusion format; the exact value could not be determined)

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'

Methods

Tested configuration: BindCraft default settings
Protocol: BindCraft best per-target binder affinity
Dataset: BindCraft binder design target PD-1
Procedure: BindCraft best per-target binder affinity
Evaluation: BindCraft best binder affinity against PD-1
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source: No interval is printed.
Evidence: Author-reported evaluation · source checkedOne-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Results 'Binders targeting cell-surface receptors', paragraph 1: 'with the best binder showing an apparent dissociation constant (Kd*) lower than 1 nM (Fig. 2a,b), although the exact Kd could not be determined due to the extremely slow dissociation rate and avidity effect from the Fc-fusion construct'

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

Reproduction

Split: Not reported
Adaptation: Not reported
Scoring implementation: binder2; apparent KD (Kd*) by BLI in a bivalent Fc-fusion format; the exact value could not be determined

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

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.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Reported result lower than 1 nM Individual claims	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ Results 'Binders targeting cell-surface receptors', paragraph 1: 'with the best binder showing an apparent dissociation constant (Kd*) lower than 1 nM (Fig. 2a,b), although the exact Kd could not be determined due to the extremely slow dissociation rate and avidity effect from the Fc-fusion construct' Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	source checked ["source-hash-verification","independent-cell-check","ai-assisted-source-review"] · 2026-10-22T15:00:00Z author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details 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. Field: `attributes.printed_value` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Extraction artifact

How to read the evidence

Sources and history

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

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: uc-binder-20261022-result-bindcraft-kd-pd1

metric: dissociation-constant
metric direction: lower
metric qualifier: binder2; apparent KD (Kd*) by BLI in a bivalent Fc-fusion format; the exact value could not be determined
missing metadata: uncertainty: note: No interval is printed.; reason: unreported
numeric value: Not reported
printed value: lower than 1 nM
printed value basis: The source states a bound or an approximate range in words rather than a fitted value.
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: Results 'Binders targeting cell-surface receptors', paragraph 1: 'with the best binder showing an apparent dissociation constant (Kd*) lower than 1 nM (Fig. 2a,b), although the exact Kd could not be determined due to the extremely slow dissociation rate and avidity effect from the Fc-fusion construct'
unit: nanomolar

Related records

evaluation: BindCraft best binder affinity against PD-1

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