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

Stable ID: use-case-mapping-binder-20261022-adaptyv-bli-binding

citation locators

locator: Sections 2.3 and 2.4; round 2 repository README, 'Experimental Workflow'; source id: uc-binder-20261022-source-adaptyv-preprint; locator: Sections 2.3 and 2.4; round 2 repository README, 'Experimental Workflow'; source id: uc-binder-20261022-source-adaptyv-repo-round2

comparison group

same-target-cross-method

comparison title

One target, one assay, many methods (EGFR)

constraints

Do not read the round-to-round change as a method effect. The design population, the ranking metric and the number of participants all changed between rounds.; Do not attribute the round-level rates to any design method. Per-method rates are not extractable from this source.; The round 1 rate is printed twice with different values, 2.5% in Section 2.4 and 3% in Section 4.2; both are recorded and neither is preferred.; The hit definition is null with a reason. Do not substitute a threshold from another protocol.

endpoint

Share of selected competition designs confirmed as binders to EGFR by a third-party automated cell-free expression and BLI pipeline

field

links:assessed_by:uc-binder-20261022-protocol-adaptyv-bli-binding

headline metric

hit-rate

limitations

No hit definition is printed anywhere in the paper.; The tested set is not a sample of any method's output: 101 of 201 round-1 and 300 of 400 round-2 designs were hand-picked by the organisers for diversity.; Entrants chose how many designs to submit and how much effort to spend, so effort is uncontrolled.; Design methods are self-declared by entrants and then curated by the organisers into five categories.; Written by the organisers, who ran the assay.; No conventional comparator arm. EGF and cetuximab were positive controls.; Preprint, not peer reviewed. No uncertainty is printed.

rationale

The only source found where designs from many methods were tested on one target, by one laboratory, on one assay, with the measurement independent of the design methods. That independence is worth more than anything else in the evidence set. What it cannot deliver is a per-method rate: the methods are the entrants' own declarations, the organisers hand-picked most of the tested set for diversity, and the three binding thresholds behind the figure counts are never defined.

reason

Add measured de novo binder design outcomes from the 2026-10-22 use-case evidence pass (#176).

relevance

direct

review

artifact sha256: 17039d69ecc37f45f6c402511b8f4497ce631003689fa95ad1ab221f8f787a4f; method: scope-review; 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; scope: Endpoint fit, relevance grade, constraints, limitations, comparison grouping and the evaluations listed in reviewed_evaluations.

reviewed evaluations

uc-binder-20261022-eval-adaptyv-bindcraft-gb1-binding; uc-binder-20261022-eval-adaptyv-both-binding; uc-binder-20261022-eval-adaptyv-r1-binding; uc-binder-20261022-eval-adaptyv-r2-binding

revision

1

source locator

uc-binder-20261022-source-adaptyv-preprint: Sections 2.3 and 2.4; round 2 repository README, 'Experimental Workflow'; uc-binder-20261022-source-adaptyv-repo-round2: Sections 2.3 and 2.4; round 2 repository README, 'Experimental Workflow'

stratum label

Adaptyv EGFR competition rounds 1 and 2

stratum order

1

value

uc-binder-20261022-protocol-adaptyv-bli-binding

pins

record id: uc-binder-20261022-eval-adaptyv-bindcraft-gb1-binding; fields: status; links; attributes.origin; attributes.comparison; sha256: 6964dac70986425e7abf48386699c91b63e3e9ba1ee40a95011b692c37067fd5; record id: uc-binder-20261022-eval-adaptyv-both-binding; fields: status; links; attributes.origin; attributes.comparison; sha256: ac39b6913e54430edcac093cc632bd5092f9fcc99e9a75607d2cc5a0ed2f080f; record id: uc-binder-20261022-eval-adaptyv-r1-binding; fields: status; links; attributes.origin; attributes.comparison; sha256: 1f625c19894483da7b807ca737da11041be5236b927df053ded7b247bd4fc534; record id: uc-binder-20261022-eval-adaptyv-r2-binding; fields: status; links; attributes.origin; attributes.comparison; sha256: 27d3dc64dd2cb19fc9bbde00076f7fb424701f26c3c0ed86595c8eea69aea952; record id: uc-binder-20261022-protocol-adaptyv-bli-binding; fields: status; name; description; facets; source_ids; links; attributes; sha256: ca69ed035c93c2bf6e66d361daa58f36f88a3330e9eab11f0fb192b04cdf4937; record id: uc-binder-20261022-result-adaptyv-bindcraft-gb1-binders; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 767f16da69e3e50a9adf47bd23bb40c71ebd5dbbc1d8d167cfc2de7565dd60d9; record id: uc-binder-20261022-result-adaptyv-both-binders-better-than-cetuximab; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 8006871e28473ac1b85f31284df4fc475f8b3c6b5be059e794cfc2488236ac8d; record id: uc-binder-20261022-result-adaptyv-both-binders-strong; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 281a288a5823eaceca42b2ad6146b3409e6ff2ea6599d0f584276a355d4f2d44; record id: uc-binder-20261022-result-adaptyv-both-binders-total; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: a6d335c4000717e1c6882da74878020e022f310938d490e41f5825eb75b3364b; record id: uc-binder-20261022-result-adaptyv-r1-binders; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 2be530f6ffc418f1e42272ea94aedad342d4d2e49b9937a06a37461cb929ddcc; record id: uc-binder-20261022-result-adaptyv-r1-hitrate; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 3e96eac3467de1afa4f73b3ed2136595de5511447993fb848762d953ce644c9d; record id: uc-binder-20261022-result-adaptyv-r1-hitrate-section-4-2; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 669cb9991fdf0f682aad1d8357b7c89c80945ddc953cb3cdda0ca3c63b58aa10; record id: uc-binder-20261022-result-adaptyv-r2-binders; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 301f87314be84d67b4afdcff924d7a3fa23dd04448f5eb62d48e70f08d05c20c; record id: uc-binder-20261022-result-adaptyv-r2-hitrate-section-4-2; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 41d9bafdbf49e1c226503033ad046187fe30365387e7a0bbfd164777ae0d428b; record id: uc-binder-20261022-source-adaptyv-preprint; fields: status; attributes.artifact_sha256; sha256: 379c0dd17d6ebf91ee5b1d65f3247c89c6c16509fc4c6a764416712b02ec8f2d; record id: uc-binder-20261022-source-adaptyv-repo-round2; fields: status; attributes.artifact_sha256; sha256: e3c1d86215efce7858743e0d5c57ce1443e3d19707a096e2e1c87c1dcc1d138b; 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

• subject: Design a new binder to a chosen target