Protocol

Adaptyv EGFR competition cell-free expression rate

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

Share of selected competition designs that expressed in Adaptyv's cell-free system.

5 evaluations · 6 results

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5 recorded evaluations, 6 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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5 evaluations · 6 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Paired BindCraft designs joined by custom linkers with a GB1 solubility tag	Protocol: Adaptyv EGFR competition cell-free expression rate Dataset: Adaptyv EGFR competition round 2 tested designs	all five showed high expression 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 Paired BindCraft designs with a GB1 tag in Adaptyv round 2: 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 of these composite designs were tested in R2; all five showed high expression but did not bind.'
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 with helical loss -2.0 as entered in Adaptyv round 2	Protocol: Adaptyv EGFR competition cell-free expression rate Dataset: Adaptyv EGFR competition round 2 tested designs	all ten 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 with helical loss -2.0 in Adaptyv round 2: 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: 'Ten out of the author's submitted beta sheeted designs were tested and - given the lower overall expression rate of the competition in R1 - surprisingly all ten showed high expression rates'
Configuration: Adaptyv EGFR competition round 1 selected submissions	Protocol: Adaptyv EGFR competition cell-free expression rate Dataset: Adaptyv EGFR competition round 1 tested designs	73% Proportion (designs expressing above the 0.02 microgram per millilitre threshold, out of designs selected for testing) percent · higher Uncertainty: Not reported by the source: No interval is printed. 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 Adaptyv EGFR competition round 1 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 2.4: 'The expression rate of 73% was about on par for the design methods commonly in the field'
Configuration: Adaptyv EGFR competition round 2 selected submissions	Protocol: Adaptyv EGFR competition cell-free expression rate Dataset: Adaptyv EGFR competition round 2 tested designs	94% Proportion (designs expressing above the 0.02 microgram per millilitre threshold, out of designs selected for testing) percent · higher Uncertainty: Not reported by the source: No interval is printed. 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 Adaptyv EGFR competition round 2 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 4.1: 'We observed an improvement in the number of designs expressed, from 73% to 94%'
Configuration: Adaptyv EGFR competition round 2 selected submissions	Protocol: Adaptyv EGFR competition cell-free expression rate Dataset: Adaptyv EGFR competition round 2 tested designs	95% Proportion (designs expressing above the 0.02 microgram per millilitre threshold, out of designs selected for testing) percent · higher Uncertainty: Not reported by the source: No interval is printed. 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 Adaptyv EGFR competition round 2 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 2.4: 'R2 saw a 95% expression rate (378 of 400 tested)'

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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-protocol-adaptyv-expression

areas: proteins-complexes; protein-structure
contexts: research
limitations: Third-party assay: Adaptyv expressed and measured the designs, so the measurement is independent of the design methods. The organisers wrote the paper.; No hit definition is printed. Section 4.1 refers to 'the 3 binding thresholds' in Figure 8 and no section of the paper defines them.; The tested set is not a sample of any method's output: half the round-1 and three quarters of the round-2 tested designs were hand-picked by the organisers for diversity, and entrants chose how many designs to submit and how much effort to spend.; Design methods are the entrants' own declarations, curated by the organisers into five categories.; Sequences yielding under 0.02 micrograms per millilitre of protein were excluded before characterisation, so the binding denominator is the expressed set for some statements and the selected set for others.; No conventional comparator arm. EGF and cetuximab were positive controls.; No uncertainty is printed for any rate.; Section 2.4 gives the round 2 expression rate as 95% (378 of 400) and Section 4.1 gives it as 94%.
metric: proportion
metric direction: higher
metric qualifier: designs that expressed above the 0.02 microgram per millilitre threshold, out of designs selected for testing
protocol: Submitted sequences are reverse-translated, codon-optimised and expressed in a cell-free system over at least two batches, with some sequences tested up to four times. Expression success is assessed by a label-free quantification assay; sequences yielding less than 0.02 micrograms per millilitre are excluded from further characterisation.
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
source locator: Sections 2.4 and 4.1; round 2 repository README, 'Protein Synthesis'
unit: percent
version: bioRxiv v1 Sections 2.3 and 2.4

Related records

assessment: Paired BindCraft designs with a GB1 tag in Adaptyv round 2: Adaptyv EGFR competition cell-free expression rate
assessment: BindCraft in Adaptyv round 1: Adaptyv EGFR competition cell-free expression rate
assessment: BindCraft with helical loss -2.0 in Adaptyv round 2: Adaptyv EGFR competition cell-free expression rate
assessment: Adaptyv EGFR competition round 1 expression rate
assessment: Adaptyv EGFR competition round 2 expression rate
assessed by: Design a new binder to a chosen target

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