Evaluation

BindCraft experimental success rate over its 12 benchmark targets

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 aggregate transcribed from the pinned source; not reproduced.

Evaluation results

1 evaluation · 2 results. Different protocols are not a single leaderboard.

Protocol: BindCraft experimental success rate averaged over its 12 benchmark targets · Dataset: BindCraft 12-target benchmark set

Sorted by Hit rate (range of per-target experimental success rates over 12 targets) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Hit rate (range of per-target experimental success rates over 12 targets)	Hit rate (unweighted mean of per-target experimental success rates over 12 targets)
BindCraft default settingsEvaluation	10% to 100%	46.3%

All 2 result rows with coverage, uncertainty and sources

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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 experimental success rate averaged over its 12 benchmark targets Dataset: BindCraft 12-target benchmark set	46.3% Hit rate (unweighted mean of per-target experimental success rates over 12 targets) percent · higher 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 experimental success rate over its 12 benchmark targets uc-binder-20261022-protocol-bindcraft-mean-success-rate-12-targets Aggregation: Not reported One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Introduction, final paragraph: 'The binder affinities lie predominantly in the nanomolar range, with success rates from 10% to 100%, with an average success rate of 46.3%'
Configuration: BindCraft default settings	Protocol: BindCraft experimental success rate averaged over its 12 benchmark targets Dataset: BindCraft 12-target benchmark set	10% to 100% Hit rate (range of per-target experimental success rates over 12 targets) percent · higher Uncertainty: Not applicable: The value is itself a range over targets, not an estimate with an interval. 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 experimental success rate over its 12 benchmark targets uc-binder-20261022-protocol-bindcraft-mean-success-rate-12-targets Aggregation: Not reported One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Introduction, final paragraph: 'with success rates from 10% to 100%'

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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Verified: Not verified

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Verified: Not verified

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Evaluation procedure

BindCraft experimental success rate averaged over its 12 benchmark targets

Configuration: BindCraft default settings
Protocol: BindCraft experimental success rate averaged over its 12 benchmark targets
Dataset: BindCraft 12-target benchmark set

origin: Author-reported evaluation
configuration: Nature 2025 version of record
adaptation: Not reported
aggregation: Unweighted mean over the 12 targets
budget: Not reported
dataset version: 12 targets, Supplementary Table 1 inputs
inputs: Target structures and hotspot residues from Supplementary Table 1
metric implementation: Per-target share of tested designs with observed binding
population: 12 targets; 6 to 53 designs tested per target
protocol id: uc-binder-20261022-protocol-bindcraft-mean-success-rate-12-targets
split: Not reported

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

Reproduction

Split: Not reported
Adaptation: Not reported
Scoring implementation: Per-target share of tested designs with observed binding

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.

20 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 ↗ Introduction, final paragraph 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 Unweighted mean over the 12 targets Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ Introduction, final paragraph 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 ↗ Introduction, final paragraph 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 12 targets, Supplementary Table 1 inputs Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ Introduction, final paragraph 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 structures 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 ↗ Introduction, final paragraph 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 Per-target share of tested designs with observed binding Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ Introduction, final paragraph 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 12 targets; 6 to 53 designs tested per target Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ Introduction, final paragraph 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-mean-success-rate-12-targets Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ Introduction, final paragraph 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 ↗ Introduction, final paragraph 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 these targets. Context-only references	One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) Original source ↗ Introduction, final paragraph 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-aggregate-12-targets

areas: proteins-complexes; protein-structure
contexts: research
comparison: adaptation: Not reported; aggregation: Unweighted mean over the 12 targets; budget: Not reported; dataset version: 12 targets, Supplementary Table 1 inputs; inputs: Target structures and hotspot residues from Supplementary Table 1; metric implementation: Per-target share of tested designs with observed binding; population: 12 targets; 6 to 53 designs tested per target; protocol id: uc-binder-20261022-protocol-bindcraft-mean-success-rate-12-targets; split: Not reported
conventional baseline: None run on these targets.
missing metadata: comparison.adaptation: note: No adaptation step.; reason: inapplicable; comparison.budget: note: Designs tested per target range from 6 to 53 and the mean is unweighted, so no single budget describes the aggregate.; reason: conflicting; comparison.split: note: A design campaign, not a train/test split.; reason: inapplicable
origin: author_reported
protocol: uc-binder-20261022-protocol-bindcraft-mean-success-rate-12-targets
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: Introduction, final paragraph
total targets: 12
version: Nature 2025 version of record

Related records

system: BindCraft default settings
assessment: BindCraft experimental success rate averaged over its 12 benchmark targets
data: BindCraft 12-target benchmark set
evaluation: BindCraft average experimental success rate over 12 targets
evaluation: BindCraft per-target experimental success rate range over 12 targets

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