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Evidence claim

Relevance of uc-binder-20261022-protocol-bindcraft-best-affinity 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 best per-target binder affinity
Relevance
Direct evidence
Endpoint
Dissociation constant of the highest-affinity BindCraft binder per target, without experimental sequence optimisation

Measured affinities on eleven targets, spanning three orders of magnitude from about 5 nM to 5.7 micromolar. Useful for the 'how good is the best design' half of the endpoint and for showing that a high hit rate does not imply a high affinity.

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; Figs. 2, 3 and 4; Extended Data Figs. 3 and 5
    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; Figs. 2, 3 and 4; Extended Data Figs. 3 and 5

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
binder-affinities
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; Figs. 2, 3 and 4; Extended Data Figs. 3 and 5

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
Affinity of the best binder found per 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; Figs. 2, 3 and 4; Extended Data Figs. 3 and 5

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
  • A best-of-subset value per target.
  • Several values are apparent constants rather than fitted monovalent constants, including a bivalent Fc-fusion measurement whose avidity inflates apparent affinity, and two values the source states only in words.
  • Mixed assays: SPR for most targets, BLI for PD-1 and CbAgo.
  • Do not compare with the AlphaProteo HTRF values.
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; Figs. 2, 3 and 4; Extended Data Figs. 3 and 5

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
Dissociation constant of the highest-affinity BindCraft binder per target, without experimental sequence optimisation
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; Figs. 2, 3 and 4; Extended Data Figs. 3 and 5

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-best-affinity
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; Figs. 2, 3 and 4; Extended Data Figs. 3 and 5

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
dissociation-constant
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; Figs. 2, 3 and 4; Extended Data Figs. 3 and 5

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
4 values
  • Developer-reported.
  • Best-of-subset; no uncertainty is printed.
  • Mixed assays and mixed construct formats.
  • Two of the eleven values are not numeric in the source ('lower than 1 nM', 'in the range of 300 nM') and are recorded with a null numeric value.
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; Figs. 2, 3 and 4; Extended Data Figs. 3 and 5

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
27 values
  • record id
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    fields
    • status
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    • attributes.origin
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    sha256
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  • record id
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    fields
    • status
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    sha256
    1899febc4c02bd9ec0f10ec81d29e1c671dc09e89b35185c31a116d72101c691
  • record id
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    fields
    • status
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    • attributes.origin
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    sha256
    924535a34141a72f0bd8e57c5ed39a71e59373f3617f6109c0b8b2df0ead3122
  • record id
    uc-binder-20261022-eval-bindcraft-affinity-cd45
    fields
    • status
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    • attributes.origin
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    sha256
    71cca41ea561eb2e141fd0277cf6bd8ba86313e63c230f3ec3d529917d2ac9dc
  • record id
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    fields
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    sha256
    784a34af40ea5896301ce0c73098f712d2bee4b70e67d3dbc5972147cb6d8267
  • record id
    uc-binder-20261022-eval-bindcraft-affinity-crsas6-dimer
    fields
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    sha256
    f3d9107af603fec9fe61bc2424684b9e7536951ea3690d465aab79d21c11541c
  • record id
    uc-binder-20261022-eval-bindcraft-affinity-derf21
    fields
    • status
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    sha256
    1ca2eecfbe866ae6870012d6c5c8e7291a1d146ac99a6a4e2ba893c17cd84a72
  • record id
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    fields
    • status
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    sha256
    19a6f407b6ee8797a777a8c93b19109b1a07c2ac86465269656d3b88328bd541
  • record id
    uc-binder-20261022-eval-bindcraft-affinity-ifnar2
    fields
    • status
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    sha256
    28420a8ff3e087513f4f37cf2068fb2cefb9828bcf84fddca52ce54caf784fc6
  • record id
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    fields
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    sha256
    ed3a26c12bcd2d34d1ff4822e9ad69e0dfd0b3345eadada17ff1727d93f49ca6
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    f8b2bc93a19f92820b1aa617c76676d059ad5efb5ffc6406999cf3350ef8e118
  • record id
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    fields
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    sha256
    e50fef13e32c04967e21d683275dc279b6f022dfe5ccc7f3387c1a091d00781b
  • record id
    uc-binder-20261022-protocol-bindcraft-best-affinity
    fields
    • status
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    • source_ids
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    sha256
    3fc535910ff24e6a3c96f001953a7402e417926304fb46087f1800d2ec9a9f3d
  • record id
    uc-binder-20261022-result-bindcraft-kd-bbf14
    fields
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    sha256
    6873e22837e7a552c8df8047112a10f0a764db3da81c2f5dd33973f097a3e1ad
  • record id
    uc-binder-20261022-result-bindcraft-kd-betv1
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    3a56845979736159b4ae70c9a3a44123012b53dd9015c778b214cf53e5b0baf4
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    uc-binder-20261022-result-bindcraft-kd-cbago
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    27d207c7ae3ef6d8e14a2b5d0aa747dd18a8e687f6ac5d00d32f81ea7e141a62
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    uc-binder-20261022-result-bindcraft-kd-cd45
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    20633d6bb4ea1f6550caffa03b60a83cee19f5ad2d594afb51de424901922bba
  • record id
    uc-binder-20261022-result-bindcraft-kd-crsas6
    fields
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    sha256
    8d0eafe506aa4e9843998b7d574d2490c4dde51c06ce0a7e1b399a573e81ca87
  • record id
    uc-binder-20261022-result-bindcraft-kd-crsas6-dimer
    fields
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    sha256
    bbd29bd0ab3869e0b7bcce7a1f90f009cfa1c0581f1a8bbf1e70beccecc5e03e
  • record id
    uc-binder-20261022-result-bindcraft-kd-derf21
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    87ce8181c7a9692397bac999d9d00e0ffb1e45a3e163b77bcc5b273bf925f46b
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    fields
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    ac5855e90d09739bf6f21b5f19f21e19677147946a1766dad35be35fd058b1a1
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    6a36e802abf1a73b1f668a8d03a63913257aa801b52551de99a9dd463c81c5df
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    8ecb5a44d6321340f3d83369e19eceaf68624116c78f0981526b29d169f97c8b
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    fields
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    sha256
    135142a16425501404d472f3ef19c65142deb3a5284f4b6be02ba48094f895e5
  • record id
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    fields
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    sha256
    d3bd9c67fe1a3b209916f330437cb5ff046ad76c4666c0976e40a65549ba279f
  • record id
    use-case-de-novo-binder-design
    fields
    • status
    • name
    • description
    • facets
    • attributes.question
    • attributes.decision
    • attributes.inputs
    • attributes.output
    • attributes.exclusions
    • attributes.setting
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    sha256
    b5a0012d1b0f02d6bd7466b7308123b26e676eda8ef54d706c865bb3f777e5b9
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; Figs. 2, 3 and 4; Extended Data Figs. 3 and 5

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 affinities on eleven targets, spanning three orders of magnitude from about 5 nM to 5.7 micromolar. Useful for the 'how good is the best design' half of the endpoint and for showing that a high hit rate does not imply a high affinity.
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; Figs. 2, 3 and 4; Extended Data Figs. 3 and 5

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-best-affinity

citation locators
locator: Fig. 1b caption; Figs. 2, 3 and 4; Extended Data Figs. 3 and 5; source id: uc-binder-20261022-source-bindcraft
comparison group
binder-affinities
comparison title
Affinity of the best binder found per target
constraints
A best-of-subset value per target.; Several values are apparent constants rather than fitted monovalent constants, including a bivalent Fc-fusion measurement whose avidity inflates apparent affinity, and two values the source states only in words.; Mixed assays: SPR for most targets, BLI for PD-1 and CbAgo.; Do not compare with the AlphaProteo HTRF values.
endpoint
Dissociation constant of the highest-affinity BindCraft binder per target, without experimental sequence optimisation
field
links:assessed_by:uc-binder-20261022-protocol-bindcraft-best-affinity
headline metric
dissociation-constant
limitations
Developer-reported.; Best-of-subset; no uncertainty is printed.; Mixed assays and mixed construct formats.; Two of the eleven values are not numeric in the source ('lower than 1 nM', 'in the range of 300 nM') and are recorded with a null numeric value.
rationale
Measured affinities on eleven targets, spanning three orders of magnitude from about 5 nM to 5.7 micromolar. Useful for the 'how good is the best design' half of the endpoint and for showing that a high hit rate does not imply a high affinity.
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-affinity-bbf14; uc-binder-20261022-eval-bindcraft-affinity-betv1; uc-binder-20261022-eval-bindcraft-affinity-cbago; uc-binder-20261022-eval-bindcraft-affinity-cd45; uc-binder-20261022-eval-bindcraft-affinity-crsas6; uc-binder-20261022-eval-bindcraft-affinity-crsas6-dimer; uc-binder-20261022-eval-bindcraft-affinity-derf21; uc-binder-20261022-eval-bindcraft-affinity-derf7; uc-binder-20261022-eval-bindcraft-affinity-ifnar2; uc-binder-20261022-eval-bindcraft-affinity-pd1; uc-binder-20261022-eval-bindcraft-affinity-pdl1; uc-binder-20261022-eval-bindcraft-affinity-spcas9
revision
1
source locator
uc-binder-20261022-source-bindcraft: Fig. 1b caption; Figs. 2, 3 and 4; Extended Data Figs. 3 and 5
stratum label
BindCraft, SPR and BLI
stratum order
2
value
uc-binder-20261022-protocol-bindcraft-best-affinity
pins
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