Evaluation

BindCraft best binder affinity against Bet v1

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'

Developer-reported outcome transcribed from the pinned source; not reproduced.

Evaluation results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: BindCraft default settings	Protocol: BindCraft best per-target binder affinity Dataset: BindCraft binder design target Bet v1	120 nM Dissociation constant (binder2; by SPR) nanomolar · lower Uncertainty: Not reported by the source: No interval is printed. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source BindCraft best binder affinity against Bet v1 uc-binder-20261022-protocol-bindcraft-best-affinity Aggregation: Not reported One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Results 'Masking allergenic epitopes', paragraph 5: 'Binder2 showed a 120 nM binding affinity by SPR'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

Evidence incomplete

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File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

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Score meaning and direction are confirmed: not yet verified
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Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

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Score meaning and direction are confirmed: not yet verified
A pinned run recipe exists: not yet verified
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Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Independent validation data exist: not yet verified
Overlap with training data is checked: not yet verified

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Evaluation procedure

BindCraft best per-target binder affinity

Configuration: BindCraft default settings
Protocol: BindCraft best per-target binder affinity
Dataset: BindCraft binder design target Bet v1

origin: Author-reported evaluation
configuration: Nature 2025 version of record
adaptation: Not reported
aggregation: Best (lowest) KD among the binders identified for the target
budget: Not reported
dataset version: Bet v1, Supplementary Table 1 input
inputs: Target structure and hotspot residues from Supplementary Table 1
metric implementation: binder2; by SPR
population: Not reported
protocol id: uc-binder-20261022-protocol-bindcraft-best-affinity
split: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Not reported
Adaptation: Not reported
Scoring implementation: binder2; by SPR

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.

19 evidence rows 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
Comparison: adaptation Not reported Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ Results 'Masking allergenic epitopes', paragraph 5: 'Binder2 showed a 120 nM binding affinity by SPR' Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	missing or unspecified No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation Best (lowest) KD among the binders identified for the target Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ Results 'Masking allergenic epitopes', paragraph 5: 'Binder2 showed a 120 nM binding affinity by SPR' Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	not individually reviewed No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ Results 'Masking allergenic epitopes', paragraph 5: 'Binder2 showed a 120 nM binding affinity by SPR' Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	missing or unspecified No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version Bet v1, Supplementary Table 1 input Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ Results 'Masking allergenic epitopes', paragraph 5: 'Binder2 showed a 120 nM binding affinity by SPR' Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	not individually reviewed No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs Target structure and hotspot residues from Supplementary Table 1 Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ Results 'Masking allergenic epitopes', paragraph 5: 'Binder2 showed a 120 nM binding affinity by SPR' Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	not individually reviewed No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: metric implementation binder2; by SPR Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ Results 'Masking allergenic epitopes', paragraph 5: 'Binder2 showed a 120 nM binding affinity by SPR' Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	not individually reviewed No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: population Not reported Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ Results 'Masking allergenic epitopes', paragraph 5: 'Binder2 showed a 120 nM binding affinity by SPR' Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	missing or unspecified No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: protocol id uc-binder-20261022-protocol-bindcraft-best-affinity Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ Results 'Masking allergenic epitopes', paragraph 5: 'Binder2 showed a 120 nM binding affinity by SPR' Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	not individually reviewed No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: split Not reported Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ Results 'Masking allergenic epitopes', paragraph 5: 'Binder2 showed a 120 nM binding affinity by SPR' Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	missing or unspecified No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Conventional baseline None run on this target. Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ Results 'Masking allergenic epitopes', paragraph 5: 'Binder2 showed a 120 nM binding affinity by SPR' Version: Nature, version of record; Europe PMC JATS full text for PMC12507698 Retrieved: 2026-10-22T11:55:00Z	not individually reviewed No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.conventional_baseline` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected 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

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Technical metadata and extraction receipts

Stable ID: uc-binder-20261022-eval-bindcraft-affinity-betv1

areas: proteins-complexes; protein-structure
contexts: research
comparison: adaptation: Not reported; aggregation: Best (lowest) KD among the binders identified for the target; budget: Not reported; dataset version: Bet v1, Supplementary Table 1 input; inputs: Target structure and hotspot residues from Supplementary Table 1; metric implementation: binder2; by SPR; population: Not reported; protocol id: uc-binder-20261022-protocol-bindcraft-best-affinity; split: Not reported
conventional baseline: None run on this target.
missing metadata: comparison.adaptation: note: Affinities are for designs without experimental sequence optimisation.; reason: inapplicable; comparison.budget: note: Not stated for the titration step.; reason: unreported; comparison.population: note: The paper does not state how many of the target's binders were titrated.; reason: unreported; comparison.split: note: A design campaign, not a train/test split.; reason: inapplicable
origin: author_reported
protocol: uc-binder-20261022-protocol-bindcraft-best-affinity
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 'Masking allergenic epitopes', paragraph 5: 'Binder2 showed a 120 nM binding affinity by SPR'
version: Nature 2025 version of record

Related records

system: BindCraft default settings
assessment: BindCraft best per-target binder affinity
data: BindCraft binder design target Bet v1
evaluation: BindCraft best binder affinity against Bet v1

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