Protocol

Adaptyv EGFR competition BLI binding screen

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 confirmed as binders to EGFR by Adaptyv's automated cell-free expression and biolayer interferometry pipeline.

4 evaluations · 9 results

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4 recorded evaluations, 9 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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4 evaluations · 9 results. Different protocols are not a single leaderboard.

Protocol: Adaptyv EGFR competition BLI binding screen

Sorted by Count (designs confirmed as binders by BLI) (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 confirmed as binders by BLI)	Count (binders the paper calls strong, in the tens of nanomolar range)	Count (binders with better affinity for EGFR than the cetuximab positive control)	Count (designs confirmed as binders by BLI across both rounds)	Count (novel binders confirmed by BLI; two further binders were disqualified for similarity to an existing EGFR binder)	Hit rate (designs confirmed as binders by BLI, out of designs selected for testing, as stated in Section 4.2; Section 2.4 prints 2.5% (5/201) for the same round)	Hit rate (designs confirmed as binders by BLI, out of designs selected for testing; the sentence gives round 1 as 3%, which does not reconcile with the 2.5% (5/201) in Section 2.4)	Hit rate (novel binders confirmed by BLI, out of designs selected for testing; excludes two binders later disqualified for similarity to an existing binder)
Adaptyv EGFR competition round 2 selected submissionsEvaluation	Adaptyv EGFR competition round 2 tested designs	53 confirmed binders (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	13%	Not reported
Paired BindCraft designs joined by custom linkers with a GB1 solubility tagEvaluation	Adaptyv EGFR competition round 2 tested designs	did not bind	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Crowdsourced EGFR binder submissions (Adaptyv competition)Evaluation	Adaptyv EGFR competition, both rounds	Not reported	4	2	60 binders	Not reported	Not reported	Not reported	Not reported
Adaptyv EGFR competition round 1 selected submissionsEvaluation	Adaptyv EGFR competition round 1 tested designs	Not reported	Not reported	Not reported	Not reported	5 novel binders (+2 disqualified binders which slipped through the similarity check to existing binders initially)	3%	Not reported	2.5% (5/201)

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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 BLI binding screen Dataset: Adaptyv EGFR competition round 2 tested designs	did not bind Count (designs confirmed as binders by BLI) 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 BLI binding screen uc-binder-20261022-protocol-adaptyv-bli-binding 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.'
Method: Crowdsourced EGFR binder submissions (Adaptyv competition)	Protocol: Adaptyv EGFR competition BLI binding screen Dataset: Adaptyv EGFR competition, both rounds	2 Count (binders with better affinity for EGFR than the cetuximab positive control) 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 Adaptyv EGFR competition total binders across both rounds uc-binder-20261022-protocol-adaptyv-bli-binding Aggregation: Not reported Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) · Section 4.2: 'Out of these, 2 had better binding affinities than the Cetuximab control in the nanomolar range.'
Method: Crowdsourced EGFR binder submissions (Adaptyv competition)	Protocol: Adaptyv EGFR competition BLI binding screen Dataset: Adaptyv EGFR competition, both rounds	4 Count (binders the paper calls strong, in the tens of nanomolar range) 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 Adaptyv EGFR competition total binders across both rounds uc-binder-20261022-protocol-adaptyv-bli-binding Aggregation: Not reported Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) · Section 4.2: 'with 4 of those as strong binders (in the tens of nM range)'
Method: Crowdsourced EGFR binder submissions (Adaptyv competition)	Protocol: Adaptyv EGFR competition BLI binding screen Dataset: Adaptyv EGFR competition, both rounds	60 binders Count (designs confirmed as binders by BLI across both rounds) 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 Adaptyv EGFR competition total binders across both rounds uc-binder-20261022-protocol-adaptyv-bli-binding Aggregation: Not reported Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) · Section 4.2: 'In total, we have amassed 60 binders, with 4 of those as strong binders (in the tens of nM range).'
Configuration: Adaptyv EGFR competition round 1 selected submissions	Protocol: Adaptyv EGFR competition BLI binding screen Dataset: Adaptyv EGFR competition round 1 tested designs	5 novel binders (+2 disqualified binders which slipped through the similarity check to existing binders initially) Count (novel binders confirmed by BLI; two further binders were disqualified for similarity to an existing EGFR binder) 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 Adaptyv EGFR competition round 1 binding rate uc-binder-20261022-protocol-adaptyv-bli-binding Aggregation: Not reported Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) · Section 2.4: 'Out of these designs, 146 expressed with 5 novel binders (+2 disqualified binders which slipped through the similarity check to existing binders initially).'
Configuration: Adaptyv EGFR competition round 1 selected submissions	Protocol: Adaptyv EGFR competition BLI binding screen Dataset: Adaptyv EGFR competition round 1 tested designs	2.5% (5/201) Hit rate (novel binders confirmed by BLI, out of designs selected for testing; excludes two binders later disqualified for similarity to an existing binder) 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 binding rate uc-binder-20261022-protocol-adaptyv-bli-binding Aggregation: Not reported Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) · Section 2.4: 'previous work on de novo binders to EGFR achieved an 0.01% hit rate versus the 2.5% (5/201) we had observed in R1'
Configuration: Adaptyv EGFR competition round 1 selected submissions	Protocol: Adaptyv EGFR competition BLI binding screen Dataset: Adaptyv EGFR competition round 1 tested designs	3% Hit rate (designs confirmed as binders by BLI, out of designs selected for testing, as stated in Section 4.2; Section 2.4 prints 2.5% (5/201) for the same round) 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 binding rate uc-binder-20261022-protocol-adaptyv-bli-binding Aggregation: Not reported Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) · Section 4.1: 'from 3% in the first round to 13% (Figure 8)'
Configuration: Adaptyv EGFR competition round 2 selected submissions	Protocol: Adaptyv EGFR competition BLI binding screen Dataset: Adaptyv EGFR competition round 2 tested designs	53 confirmed binders Count (designs confirmed as binders by BLI) 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 Adaptyv EGFR competition round 2 binding rate uc-binder-20261022-protocol-adaptyv-bli-binding 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) as well as a much higher binding rate with 53 confirmed binders'
Configuration: Adaptyv EGFR competition round 2 selected submissions	Protocol: Adaptyv EGFR competition BLI binding screen Dataset: Adaptyv EGFR competition round 2 tested designs	13% Hit rate (designs confirmed as binders by BLI, out of designs selected for testing; the sentence gives round 1 as 3%, which does not reconcile with the 2.5% (5/201) in Section 2.4) 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 binding rate uc-binder-20261022-protocol-adaptyv-bli-binding Aggregation: Not reported Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition (Cotet et al., bioRxiv 2025) · Section 4.1: 'Another exciting improvement has been in the percentage of successful binders to EGFR, from 3% in the first round to 13% (Figure 8)'

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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-bli-binding

areas: proteins-complexes; protein-structure
contexts: research
control: EGF and cetuximab as positive controls; cetuximab measured 9.94 nM in this assay.
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.
metric: hit-rate
metric direction: higher
metric qualifier: designs confirmed as binders to EGFR by BLI, out of designs selected for testing
missing metadata: success threshold: note: Section 4.1 refers to Figure 8 reporting binders 'across the 3 binding thresholds' and the body never defines them. No threshold is recorded and none is inferred.; reason: unreported
protocol: Submitted sequences are reverse-translated and codon-optimised, expressed in a cell-free system in at least two batches, and quantified by a label-free assay. Sequences yielding less than 0.02 micrograms per millilitre are excluded. Expressed ligands are immobilised by tag-specific chemistry and EGFR is flowed over the probe at 1000 nM to 10 nM in a multi-cycle kinetic assay, in duplicate, in HBS-T with 0.5% BSA at 25 degrees Celsius. Signals are baseline-corrected and fitted with a 1:1 binding model; where the maximum signal is below the quantifiable threshold or the kinetics are too fast, equilibrium analysis is used instead. A minimum of two replicates was run for each design, and EGF and cetuximab were run as positive controls.
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 bias: Half the round-1 and three quarters of the round-2 tested designs were hand-picked by the organisers for diversity.
source locator: Sections 2.3 and 2.4; round 2 repository README, 'Experimental Workflow'
unit: percent
version: bioRxiv v1 Section 2.3; round 2 repository README Methods at commit fc91b91ddc367830b755b215dbc69669675ad6a0

Related records

assessment: Paired BindCraft designs with a GB1 tag in Adaptyv round 2: Adaptyv EGFR competition BLI binding screen
assessment: Adaptyv EGFR competition total binders across both rounds
assessment: Adaptyv EGFR competition round 1 binding rate
assessment: Adaptyv EGFR competition round 2 binding rate
assessed by: Design a new binder to a chosen target

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