Evaluation

BindCraft binding screen 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 per-target binding screen, hit where a binding signal was observed Dataset: BindCraft binder design target Bet v1	two successful designs Count (designs with an observed binding signal (SPR), out of designs tested) count · higher Uncertainty: Not applicable: An exact count. 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 binding screen against Bet v1 uc-binder-20261022-protocol-bindcraft-binding-screen Aggregation: Not reported One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Results 'Masking allergenic epitopes', paragraph 5: 'we identified two successful designs from seven tested binders against the birch allergen Bet v1 (Fig. 1b)'

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

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Readiness checks, gaps and artifacts

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

Evidence incomplete

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Missing or unresolved evidence

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File checksums match the recorded files: not yet verified
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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

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Missing or unresolved evidence

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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
Sample annotations are recorded: not yet verified
Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

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Missing or unresolved evidence

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Score meaning and direction are confirmed: 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
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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 per-target binding screen, hit where a binding signal was observed

Configuration: BindCraft default settings
Protocol: BindCraft per-target binding screen, hit where a binding signal was observed
Dataset: BindCraft binder design target Bet v1

origin: Author-reported evaluation
configuration: Nature 2025 version of record
adaptation: Not reported
aggregation: Count per target
budget: 7 designs expressed, purified and assayed
dataset version: Bet v1, Supplementary Table 1 input
inputs: Target structure and hotspot residues from Supplementary Table 1
metric implementation: Count of tested designs with an observed binding signal (SPR)
population: 7 BindCraft designs tested against Bet v1
protocol id: uc-binder-20261022-protocol-bindcraft-binding-screen
split: Not reported

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

Reproduction

Split: Not reported
Adaptation: Not reported
Scoring implementation: Count of tested designs with an observed binding signal (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.

22 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
Candidate selection About 10 designs from the top 20 ranked by the pipeline's own i_pTM score. 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: 'we identified two successful designs from seven tested binders against the birch allergen Bet v1 (Fig. 1b)' 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.candidate_selection` Source artifact SHA-256: `74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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: 'we identified two successful designs from seven tested binders against the birch allergen Bet v1 (Fig. 1b)' 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 Count per 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: 'we identified two successful designs from seven tested binders against the birch allergen Bet v1 (Fig. 1b)' 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 7 designs expressed, purified and assayed 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: 'we identified two successful designs from seven tested binders against the birch allergen Bet v1 (Fig. 1b)' 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.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: 'we identified two successful designs from seven tested binders against the birch allergen Bet v1 (Fig. 1b)' 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: 'we identified two successful designs from seven tested binders against the birch allergen Bet v1 (Fig. 1b)' 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 Count of tested designs with an observed binding signal (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: 'we identified two successful designs from seven tested binders against the birch allergen Bet v1 (Fig. 1b)' 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 7 BindCraft designs tested against Bet v1 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: 'we identified two successful designs from seven tested binders against the birch allergen Bet v1 (Fig. 1b)' 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.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-binding-screen 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: 'we identified two successful designs from seven tested binders against the birch allergen Bet v1 (Fig. 1b)' 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: 'we identified two successful designs from seven tested binders against the birch allergen Bet v1 (Fig. 1b)' 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

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-screen-betv1

areas: proteins-complexes; protein-structure
contexts: research
candidate selection: About 10 designs from the top 20 ranked by the pipeline's own i_pTM score.
comparison: adaptation: Not reported; aggregation: Count per target; budget: 7 designs expressed, purified and assayed; dataset version: Bet v1, Supplementary Table 1 input; inputs: Target structure and hotspot residues from Supplementary Table 1; metric implementation: Count of tested designs with an observed binding signal (SPR); population: 7 BindCraft designs tested against Bet v1; protocol id: uc-binder-20261022-protocol-bindcraft-binding-screen; split: Not reported
conventional baseline: None run on this target.
denominator: 7
endpoint: Binding signal observed by SPR
missing metadata: comparison.adaptation: note: No adaptation step.; reason: inapplicable; comparison.split: note: A design campaign, not a train/test split.; reason: inapplicable
origin: author_reported
protocol: uc-binder-20261022-protocol-bindcraft-binding-screen
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: 'we identified two successful designs from seven tested binders against the birch allergen Bet v1 (Fig. 1b)'
version: Nature 2025 version of record

Related records

system: BindCraft default settings
assessment: BindCraft per-target binding screen, hit where a binding signal was observed
data: BindCraft binder design target Bet v1
evaluation: BindCraft designs with observed binding against Bet v1

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