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Evidence claim

Relevance of uc-binder-20261022-protocol-bindcraft-binding-screen to "Which computational design workflow produces binders that work when they are made and tested?"

Use case
Design a new binder to a chosen target
Assessed by
BindCraft per-target binding screen, hit where a binding signal was observed
Relevance
Direct evidence
Endpoint
Number of tested BindCraft designs with an observed binding signal, per target, with the number of designs tested

Measured wet-lab binding outcomes on ten of BindCraft's twelve benchmark targets, each with the design denominator stated in the Results prose. It is the per-target spread the use case needs, and it is what the headline 46.3% average is built from.

12 reviewed evaluations

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 statementOriginal source and locationReview and provenance
Citation locations
1 values
  • locator
    Fig. 1b caption; Results sections 'Binders targeting cell-surface receptors', 'Targeting unexplored binding sites', 'Masking allergenic epitopes' and 'Modulating multi-domain nucleases'
    source id
    uc-binder-20261022-source-bindcraft
Context-only references		One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025)

Original source ↗

uc-binder-20261022-source-bindcraft: Fig. 1b caption; Results sections 'Binders targeting cell-surface receptors', 'Targeting unexplored binding sites', 'Masking allergenic epitopes' and 'Modulating multi-domain nucleases'

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

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.citation_locators

Source artifact SHA-256: 74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison group
miniprotein-binder-hit-rates
Context-only references		One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025)

Original source ↗

uc-binder-20261022-source-bindcraft: Fig. 1b caption; Results sections 'Binders targeting cell-surface receptors', 'Targeting unexplored binding sites', 'Masking allergenic epitopes' and 'Modulating multi-domain nucleases'

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

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.comparison_group

Source artifact SHA-256: 74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison title
Miniprotein binder hit rates by target
Context-only references		One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025)

Original source ↗

uc-binder-20261022-source-bindcraft: Fig. 1b caption; Results sections 'Binders targeting cell-surface receptors', 'Targeting unexplored binding sites', 'Masking allergenic epitopes' and 'Modulating multi-domain nucleases'

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

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.comparison_title

Source artifact SHA-256: 74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Constraints
4 values
  • These are counts, not rates: the paper prints no per-target rate, so no rate is recorded.
  • The assay is not uniform across targets. Treating the ten targets as one comparison mixes SPR titration, a BLI screen in a bivalent Fc-fusion format, and an SPR prescreen against soluble analogues of the target.
  • Do not compare these counts with the AlphaProteo or Bennett rates; the endpoints differ.
  • Read each count with its denominator. They range from 6 to 53 designs.
Context-only references		One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025)

Original source ↗

uc-binder-20261022-source-bindcraft: Fig. 1b caption; Results sections 'Binders targeting cell-surface receptors', 'Targeting unexplored binding sites', 'Masking allergenic epitopes' and 'Modulating multi-domain nucleases'

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

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.constraints

Source artifact SHA-256: 74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Endpoint
Number of tested BindCraft designs with an observed binding signal, per target, with the number of designs tested
Context-only references		One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025)

Original source ↗

uc-binder-20261022-source-bindcraft: Fig. 1b caption; Results sections 'Binders targeting cell-surface receptors', 'Targeting unexplored binding sites', 'Masking allergenic epitopes' and 'Modulating multi-domain nucleases'

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

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.endpoint

Source artifact SHA-256: 74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Claimed field
links:assessed_by: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 ↗

uc-binder-20261022-source-bindcraft: Fig. 1b caption; Results sections 'Binders targeting cell-surface receptors', 'Targeting unexplored binding sites', 'Masking allergenic epitopes' and 'Modulating multi-domain nucleases'

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

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.field

Source artifact SHA-256: 74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Headline metric
count
Context-only references		One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025)

Original source ↗

uc-binder-20261022-source-bindcraft: Fig. 1b caption; Results sections 'Binders targeting cell-surface receptors', 'Targeting unexplored binding sites', 'Masking allergenic epitopes' and 'Modulating multi-domain nucleases'

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

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.headline_metric

Source artifact SHA-256: 74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Limitations
6 values
  • Developer-reported: the authors built the pipeline, chose the targets and chose which designs to test.
  • No numeric binding threshold is stated. A hit is a binding signal that was observed.
  • The designs tested are about ten of the top twenty ranked by the pipeline's own i_pTM score, so design and selection are coupled.
  • Two of the twelve targets, CrSAS-6 and CbAgo, have a stated denominator but no stated numerator; their numerators are printed only inside the Fig. 1b graphic, which was not read.
  • No conventional comparator was run.
  • No uncertainty is printed.
Context-only references		One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025)

Original source ↗

uc-binder-20261022-source-bindcraft: Fig. 1b caption; Results sections 'Binders targeting cell-surface receptors', 'Targeting unexplored binding sites', 'Masking allergenic epitopes' and 'Modulating multi-domain nucleases'

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

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.limitations

Source artifact SHA-256: 74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Pinned records
25 values
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Context-only references		One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025)

Original source ↗

uc-binder-20261022-source-bindcraft: Fig. 1b caption; Results sections 'Binders targeting cell-surface receptors', 'Targeting unexplored binding sites', 'Masking allergenic epitopes' and 'Modulating multi-domain nucleases'

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

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.pins

Source artifact SHA-256: 74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Rationale
Measured wet-lab binding outcomes on ten of BindCraft's twelve benchmark targets, each with the design denominator stated in the Results prose. It is the per-target spread the use case needs, and it is what the headline 46.3% average is built from.
Context-only references		One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025)

Original source ↗

uc-binder-20261022-source-bindcraft: Fig. 1b caption; Results sections 'Binders targeting cell-surface receptors', 'Targeting unexplored binding sites', 'Masking allergenic epitopes' and 'Modulating multi-domain nucleases'

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

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.rationale

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 historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: use-case-mapping-binder-20261022-bindcraft-binding-screen

citation locators
locator: Fig. 1b caption; Results sections 'Binders targeting cell-surface receptors', 'Targeting unexplored binding sites', 'Masking allergenic epitopes' and 'Modulating multi-domain nucleases'; source id: uc-binder-20261022-source-bindcraft
comparison group
miniprotein-binder-hit-rates
comparison title
Miniprotein binder hit rates by target
constraints
These are counts, not rates: the paper prints no per-target rate, so no rate is recorded.; The assay is not uniform across targets. Treating the ten targets as one comparison mixes SPR titration, a BLI screen in a bivalent Fc-fusion format, and an SPR prescreen against soluble analogues of the target.; Do not compare these counts with the AlphaProteo or Bennett rates; the endpoints differ.; Read each count with its denominator. They range from 6 to 53 designs.
endpoint
Number of tested BindCraft designs with an observed binding signal, per target, with the number of designs tested
field
links:assessed_by:uc-binder-20261022-protocol-bindcraft-binding-screen
headline metric
count
limitations
Developer-reported: the authors built the pipeline, chose the targets and chose which designs to test.; No numeric binding threshold is stated. A hit is a binding signal that was observed.; The designs tested are about ten of the top twenty ranked by the pipeline's own i_pTM score, so design and selection are coupled.; Two of the twelve targets, CrSAS-6 and CbAgo, have a stated denominator but no stated numerator; their numerators are printed only inside the Fig. 1b graphic, which was not read.; No conventional comparator was run.; No uncertainty is printed.
rationale
Measured wet-lab binding outcomes on ten of BindCraft's twelve benchmark targets, each with the design denominator stated in the Results prose. It is the per-target spread the use case needs, and it is what the headline 46.3% average is built from.
reason
Add measured de novo binder design outcomes from the 2026-10-22 use-case evidence pass (#176).
relevance
direct
review
artifact sha256: 74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d; method: scope-review; 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; scope: Endpoint fit, relevance grade, constraints, limitations, comparison grouping and the evaluations listed in reviewed_evaluations.
reviewed evaluations
uc-binder-20261022-eval-bindcraft-screen-bbf14; uc-binder-20261022-eval-bindcraft-screen-betv1; uc-binder-20261022-eval-bindcraft-screen-cbago; uc-binder-20261022-eval-bindcraft-screen-cd45; uc-binder-20261022-eval-bindcraft-screen-cldn1; uc-binder-20261022-eval-bindcraft-screen-crsas6; uc-binder-20261022-eval-bindcraft-screen-derf21; uc-binder-20261022-eval-bindcraft-screen-derf7; uc-binder-20261022-eval-bindcraft-screen-ifnar2; uc-binder-20261022-eval-bindcraft-screen-pd1; uc-binder-20261022-eval-bindcraft-screen-pdl1; uc-binder-20261022-eval-bindcraft-screen-spcas9
revision
1
source locator
uc-binder-20261022-source-bindcraft: Fig. 1b caption; Results sections 'Binders targeting cell-surface receptors', 'Targeting unexplored binding sites', 'Masking allergenic epitopes' and 'Modulating multi-domain nucleases'
stratum label
BindCraft per-target binding screens
stratum order
3
value
uc-binder-20261022-protocol-bindcraft-binding-screen
pins
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