Configuration

BindCraft default settings as entered in Adaptyv round 1

Evidence concern: excluded from comparisons

The paper prints three different round-1 binder rates and two round-2 expression rates. Section 2.4 gives round 1 as '2.5% (5/201)' and round 2 as 'a 95% expression rate (378 of 400 tested)'; Section 4.1 gives expression as improving 'from 73% to 94%'; Section 4.1 gives the binder percentage as rising 'from 3% in the first round to 13%'. All the printed values are recorded with their locators and none is reconciled here.Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) · Sections 2.4, 4.1 and 4.2

Section 4.1 says Figure 8 shows 'the total number of validated binders across the 3 binding thresholds' but no section of the paper defines those three thresholds. No hit definition is therefore recorded for the Figure 8 counts, and the binding protocol's success threshold is left unstated with a reason rather than guessed.Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) · Section 4.1; Figure 8 caption

BindCraft run by its own authors with the published default settings against the beta-sheeted interface of EGFR, with the top-scoring designs selected by AlphaFold2 ipTM.

2 evaluations · 2 results

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Evaluations and results

2 evaluations · 2 results. Different protocols are not a single leaderboard.

Dataset: Adaptyv EGFR competition round 1 tested designs

Sorted by Count (designs with high expression) (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	Protocol and dataset	Count (designs with high expression)	Dissociation constant (best KD for EGFR by BLI among the round 1 BindCraft entries; the strongest binding affinity in round 1)
BindCraft default settings as entered in Adaptyv round 1Evaluation	Adaptyv EGFR competition cell-free expression rate	Four of those showed high expression rates	Not reported
BindCraft default settings as entered in Adaptyv round 1Evaluation	Adaptyv EGFR competition BLI affinity	Not reported	491 nM

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: BindCraft default settings as entered in Adaptyv round 1	Protocol: Adaptyv EGFR competition cell-free expression rate Dataset: Adaptyv EGFR competition round 1 tested designs	Four of those showed high expression rates Count (designs with high expression) count · higher Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The paper prints three different round-1 binder rates and two round-2 expression rates. Section 2.4 gives round 1 as '2.5% (5/201)' and round 2 as 'a 95% expression rate (378 of 400 tested)'; Section 4.1 gives expression as improving 'from 73% to 94%'; Section 4.1 gives the binder percentage as rising 'from 3% in the first round to 13%'. All the printed values are recorded with their locators and none is reconciled here.Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) · Sections 2.4, 4.1 and 4.2 Section 4.1 says Figure 8 shows 'the total number of validated binders across the 3 binding thresholds' but no section of the paper defines those three thresholds. No hit definition is therefore recorded for the Figure 8 counts, and the binding protocol's success threshold is left unstated with a reason rather than guessed.Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) · Section 4.1; Figure 8 caption Methods, coverage and source BindCraft in Adaptyv round 1: Adaptyv EGFR competition cell-free expression rate uc-binder-20261022-protocol-adaptyv-expression Aggregation: Not reported Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) · Section 3.1: 'five were selected for evaluation. Four of those showed high expression rates'
Configuration: BindCraft default settings as entered in Adaptyv round 1	Protocol: Adaptyv EGFR competition BLI affinity Dataset: Adaptyv EGFR competition round 1 tested designs	491 nM Dissociation constant (best KD for EGFR by BLI among the round 1 BindCraft entries; the strongest binding affinity in round 1) nanomolar · lower Uncertainty: Not reported by the source: No interval is printed for this value in the prose; the repository records per-replicate fits. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The paper prints three different round-1 binder rates and two round-2 expression rates. Section 2.4 gives round 1 as '2.5% (5/201)' and round 2 as 'a 95% expression rate (378 of 400 tested)'; Section 4.1 gives expression as improving 'from 73% to 94%'; Section 4.1 gives the binder percentage as rising 'from 3% in the first round to 13%'. All the printed values are recorded with their locators and none is reconciled here.Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) · Sections 2.4, 4.1 and 4.2 Section 4.1 says Figure 8 shows 'the total number of validated binders across the 3 binding thresholds' but no section of the paper defines those three thresholds. No hit definition is therefore recorded for the Figure 8 counts, and the binding protocol's success threshold is left unstated with a reason rather than guessed.Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) · Section 4.1; Figure 8 caption Methods, coverage and source BindCraft in Adaptyv round 1: Adaptyv EGFR competition BLI affinity uc-binder-20261022-protocol-adaptyv-bli-affinity Aggregation: Not reported Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) · Section 3.1: 'one exhibited the strongest binding affinity in this round of the competition at 491 nM'

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) · Original source · bioRxiv preprint version 1

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Technical metadata and extraction receipts

Stable ID: uc-binder-20261022-config-adaptyv-bindcraft-r1

areas: proteins-complexes; protein-structure
contexts: research
method types: specialist
access reuse: Entered by the BindCraft authors; tested by Adaptyv.
foundation model eligible: false
method role: design
parameters: Default settings, targeting the beta-sheeted interface of EGFR; top-scoring binders by AlphaFold2 ipTM, mostly helical
reported name: BindCraft
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
selection: Five designs selected for evaluation by the authors.
source locator: Section 3.1
version: As entered in Adaptyv EGFR competition round 1

Related records

configuration of: BindCraft
system: BindCraft in Adaptyv round 1: Adaptyv EGFR competition BLI affinity
system: BindCraft in Adaptyv round 1: Adaptyv EGFR competition cell-free expression rate

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