Baseline for the de novo binder design use case
Baseline of Design a new binder to a chosen target
Directed evolution, display selection or grafting
Directed evolution, library display selection and grafting from a known complex are the established routes to a new binder that a design workflow has to beat. No source retrieved in this pass runs any of them as an arm on the same targets as a design method, so the baseline is named and recorded as unmeasured.
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.
33 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field baseline Context-only references | Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) Adaptyv preprint Sections 2.3 and 3.2 (EGF and cetuximab as positive controls; cetuximab at 9.94 nM); Bennett 2025 Discussion (contrast with yeast display selection from random libraries); AlphaProteo Table 1 caption ('Binders derived from selection-based methods, such as antibodies and nanobodies, are not considered here') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of a mutable web page. The hash describes that retrieval, not a stable artifact. |
| Claimed field baseline Context-only references | De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) Adaptyv preprint Sections 2.3 and 3.2 (EGF and cetuximab as positive controls; cetuximab at 9.94 nM); Bennett 2025 Discussion (contrast with yeast display selection from random libraries); AlphaProteo Table 1 caption ('Binders derived from selection-based methods, such as antibodies and nanobodies, are not considered here') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. |
| Claimed field baseline Context-only references | Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) Adaptyv preprint Sections 2.3 and 3.2 (EGF and cetuximab as positive controls; cetuximab at 9.94 nM); Bennett 2025 Discussion (contrast with yeast display selection from random libraries); AlphaProteo Table 1 caption ('Binders derived from selection-based methods, such as antibodies and nanobodies, are not considered here') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature, version of record; Europe PMC JATS full text for PMC12727541 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Method ids1 values
| Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) Adaptyv preprint Sections 2.3 and 3.2 (EGF and cetuximab as positive controls; cetuximab at 9.94 nM); Bennett 2025 Discussion (contrast with yeast display selection from random libraries); AlphaProteo Table 1 caption ('Binders derived from selection-based methods, such as antibodies and nanobodies, are not considered here') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of a mutable web page. The hash describes that retrieval, not a stable artifact. |
Method ids1 values
| De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) Adaptyv preprint Sections 2.3 and 3.2 (EGF and cetuximab as positive controls; cetuximab at 9.94 nM); Bennett 2025 Discussion (contrast with yeast display selection from random libraries); AlphaProteo Table 1 caption ('Binders derived from selection-based methods, such as antibodies and nanobodies, are not considered here') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. |
Method ids1 values
| Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) Adaptyv preprint Sections 2.3 and 3.2 (EGF and cetuximab as positive controls; cetuximab at 9.94 nM); Bennett 2025 Discussion (contrast with yeast display selection from random libraries); AlphaProteo Table 1 caption ('Binders derived from selection-based methods, such as antibodies and nanobodies, are not considered here') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature, version of record; Europe PMC JATS full text for PMC12727541 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records4 values
| Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) Adaptyv preprint Sections 2.3 and 3.2 (EGF and cetuximab as positive controls; cetuximab at 9.94 nM); Bennett 2025 Discussion (contrast with yeast display selection from random libraries); AlphaProteo Table 1 caption ('Binders derived from selection-based methods, such as antibodies and nanobodies, are not considered here') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of a mutable web page. The hash describes that retrieval, not a stable artifact. |
Pinned records4 values
| De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) Adaptyv preprint Sections 2.3 and 3.2 (EGF and cetuximab as positive controls; cetuximab at 9.94 nM); Bennett 2025 Discussion (contrast with yeast display selection from random libraries); AlphaProteo Table 1 caption ('Binders derived from selection-based methods, such as antibodies and nanobodies, are not considered here') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv version 1, posted 2024-09-12; full-text PDF (49 pages) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the arXiv v1 PDF on 2026-10-22. |
Pinned records4 values
| Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) Adaptyv preprint Sections 2.3 and 3.2 (EGF and cetuximab as positive controls; cetuximab at 9.94 nM); Bennett 2025 Discussion (contrast with yeast display selection from random libraries); AlphaProteo Table 1 caption ('Binders derived from selection-based methods, such as antibodies and nanobodies, are not considered here') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature, version of record; Europe PMC JATS full text for PMC12727541 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Rationale Before machine-learning design, a new binder to a chosen target came from iterated selection: directed evolution, phage or yeast display from a naive or immunised library, or grafting a known binding motif from a solved complex. Those are what a design workflow replaces, so they are the reference. The evidence this pass retrieved contains no such arm on any target a design method was also run on. Its only same-assay trace is cetuximab, an approved antibody obtained by conventional discovery, measured at 9.94 nM as a positive control in the Adaptyv EGFR assay, and AlphaProteo's Table 1 caption states that 'binders derived from selection-based methods, such as antibodies and nanobodies, are not considered here'. The baseline is therefore recorded as named but unmeasured, and the absence of a comparator is the use case's primary evidence gap. Context-only references | Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) Adaptyv preprint Sections 2.3 and 3.2 (EGF and cetuximab as positive controls; cetuximab at 9.94 nM); Bennett 2025 Discussion (contrast with yeast display selection from random libraries); AlphaProteo Table 1 caption ('Binders derived from selection-based methods, such as antibodies and nanobodies, are not considered here') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of a mutable web page. The hash describes that retrieval, not a stable artifact. |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
3 source records and release history
- Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) · Original source · bioRxiv preprint version 1
- Atomically accurate de novo design of antibodies with RFdiffusion (Bennett et al., Nature 2025) · Original source · Nature, version of record; Europe PMC JATS full text for PMC12727541
- De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Original source · arXiv version 1, posted 2024-09-12; full-text PDF (49 pages)
Technical metadata and extraction receipts
Stable ID: use-case-baseline-binder-20261022
- field
- baseline
- method ids
- uc-binder-20261022-method-conventional-binder-discovery
- rationale
- Before machine-learning design, a new binder to a chosen target came from iterated selection: directed evolution, phage or yeast display from a naive or immunised library, or grafting a known binding motif from a solved complex. Those are what a design workflow replaces, so they are the reference. The evidence this pass retrieved contains no such arm on any target a design method was also run on. Its only same-assay trace is cetuximab, an approved antibody obtained by conventional discovery, measured at 9.94 nM as a positive control in the Adaptyv EGFR assay, and AlphaProteo's Table 1 caption states that 'binders derived from selection-based methods, such as antibodies and nanobodies, are not considered here'. The baseline is therefore recorded as named but unmeasured, and the absence of a comparator is the use case's primary evidence gap.
- reason
- Name the use case's pre-machine-learning comparator for the 2026-10-22 evidence pass (#176).
- review
- artifact sha256: 17039d69ecc37f45f6c402511b8f4497ce631003689fa95ad1ab221f8f787a4f; method: source-hash-verification; independent-cell-check; ai-assisted-source-review; method note: Re-downloaded (HTTP 200, 493,217 bytes, the same byte count as the pinned retrieval) but the SHA-256 differs, as expected for a mutable bioRxiv page whose hash describes one retrieval. Every extracted value and every quoted sentence was then located verbatim in the new retrieval, so the difference is in page furniture and not in the evidence. One section attribution and one quotation were corrected.; 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.biorxiv.org/content/10.1101/2025.04.17.648362v1.full; reviewed at: 2026-10-22T15:00:00Z; reviewer: claude; reviewer note: Claude review agent, independent of the extraction agent; no human review claimed
- revision
- 1
- source locator
- Adaptyv preprint Sections 2.3 and 3.2 (EGF and cetuximab as positive controls; cetuximab at 9.94 nM); Bennett 2025 Discussion (contrast with yeast display selection from random libraries); AlphaProteo Table 1 caption ('Binders derived from selection-based methods, such as antibodies and nanobodies, are not considered here')
- value
- Directed evolution, display selection or grafting
- pins
- record id: uc-binder-20261022-source-adaptyv-preprint; fields: status; attributes.artifact_sha256; sha256: 379c0dd17d6ebf91ee5b1d65f3247c89c6c16509fc4c6a764416712b02ec8f2d; record id: uc-binder-20261022-source-alphaproteo; fields: status; attributes.artifact_sha256; sha256: 4f4d69e2483d41e1016f2b3c6f078632280b3ca9ada6ac9f76e5ad7c16c914a0; record id: uc-binder-20261022-source-bennett; fields: status; attributes.artifact_sha256; sha256: 67767c4e09155df3488e2ce80dcb47410db9ba4912be584cd0fab0d01bf6d077; 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; attributes.clinical_scope; attributes.intended_users; sha256: b5a0012d1b0f02d6bd7466b7308123b26e676eda8ef54d706c865bb3f777e5b9