Protocol

BindCraft per-target binding screen, hit where a binding signal was observed

Evidence concern: excluded from comparisons

Supplementary Data 1 has one row per tested design with a Binding column holding 1, 0 or an empty cell. Treating the non-empty cells as the tested set reproduces the prose counts for BBF-14 (11 tested, 6 binding), Bet v1 (7, 2), CD45 (16, 4), Der f7 (10, 4), Der f21 (7, 4), IFNAR2 (9, 3), PD-1 (53, 13), SpCas9 (6, 6) and CLDN1 (7, 6), but not for PD-L1 (13 non-empty rows with 11 binding against 9 tested with 7 binding in the prose), CrSAS-6 (10 non-empty rows against 9 tested) or CbAgo (2 non-empty rows against 12 tested). The row filter is therefore ambiguous and no value is computed from these rows.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Results prose; Fig. 1b caption

Fig. 1b's caption defines success as binding observed on SPR, but the PD-1 screen was BLI in a bivalent Fc-fusion format and the CLDN1 screen used soluble analogues. The 46.3% average therefore pools targets measured under different endpoints.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Fig. 1b caption; Results 'Binders targeting cell-surface receptors' and 'Targeting unexplored binding sites'

Number of tested BindCraft designs for which a binding signal was observed in the paper's per-target screen, out of the designs tested.

10 evaluations · 10 results

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

10 recorded evaluations, 10 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

10 evaluations · 10 results. Different protocols are not a single leaderboard.

Protocol: BindCraft per-target binding screen, hit where a binding signal was observed

Sorted by Count (designs with an observed binding signal (SPR), out of designs tested) (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 an observed binding signal (SPR), out of designs tested)	Count (designs with an observed binding signal (BLI, bivalent Fc-fusion format), out of designs tested)	Count (designs with an observed binding signal (SPR against full-length apo SpCas9), out of designs tested)	Count (designs with an observed binding signal (SPR prescreen at 10 micromolar against immobilised PD-L1-Fc, then SPR titration), out of designs tested)	Count (designs with an observed binding signal (SPR prescreen at 10 micromolar against immobilised soluble claudin-1 analogues), out of designs tested)
BindCraft default settingsEvaluation	BindCraft binder design target BBF-14	6 showed binding (best in column)	Not reported	Not reported	Not reported	Not reported
BindCraft default settingsEvaluation	BindCraft binder design target CD45	4 showed binding on SPR	Not reported	Not reported	Not reported	Not reported
BindCraft default settingsEvaluation	BindCraft binder design target Der f21	detect binding for four designs by SPR	Not reported	Not reported	Not reported	Not reported
BindCraft default settingsEvaluation	BindCraft binder design target Der f7	identified 4 binders	Not reported	Not reported	Not reported	Not reported
BindCraft default settingsEvaluation	BindCraft binder design target IFNAR2	binding for three out of nine designs	Not reported	Not reported	Not reported	Not reported
BindCraft default settingsEvaluation	BindCraft binder design target Bet v1	two successful designs	Not reported	Not reported	Not reported	Not reported
BindCraft default settingsEvaluation	BindCraft binder design target Claudin1	Not reported	Not reported	Not reported	Not reported	all except binder17 to bind to sCLDN1-14 and sCLDN1-18
BindCraft default settingsEvaluation	BindCraft binder design target PD-1	Not reported	a binding signal for 13 binders	Not reported	Not reported	Not reported
BindCraft default settingsEvaluation	BindCraft binder design target PD-L1	Not reported	Not reported	Not reported	seven showed a binding signal	Not reported
BindCraft default settingsEvaluation	BindCraft binder design target SpCas9	Not reported	Not reported	All six tested binders bound the full-length apo SpCas9 enzyme	Not reported	Not reported

All 10 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: BindCraft default settings	Protocol: BindCraft per-target binding screen, hit where a binding signal was observed Dataset: BindCraft binder design target BBF-14	6 showed binding Count (designs with an observed binding signal (SPR), out of designs tested) count · higher Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Data 1 has one row per tested design with a Binding column holding 1, 0 or an empty cell. Treating the non-empty cells as the tested set reproduces the prose counts for BBF-14 (11 tested, 6 binding), Bet v1 (7, 2), CD45 (16, 4), Der f7 (10, 4), Der f21 (7, 4), IFNAR2 (9, 3), PD-1 (53, 13), SpCas9 (6, 6) and CLDN1 (7, 6), but not for PD-L1 (13 non-empty rows with 11 binding against 9 tested with 7 binding in the prose), CrSAS-6 (10 non-empty rows against 9 tested) or CbAgo (2 non-empty rows against 12 tested). The row filter is therefore ambiguous and no value is computed from these rows.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Results prose; Fig. 1b caption Fig. 1b's caption defines success as binding observed on SPR, but the PD-1 screen was BLI in a bivalent Fc-fusion format and the CLDN1 screen used soluble analogues. The 46.3% average therefore pools targets measured under different endpoints.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Fig. 1b caption; Results 'Binders targeting cell-surface receptors' and 'Targeting unexplored binding sites' Methods, coverage and source BindCraft binding screen against BBF-14 uc-binder-20261022-protocol-bindcraft-binding-screen Aggregation: Not reported One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Results 'Targeting unexplored binding sites', paragraph 3: 'We purified the 11 top-scoring designs from which 6 showed binding (Fig. 1b)'
Configuration: BindCraft default settings	Protocol: BindCraft per-target binding screen, hit where a binding signal was observed Dataset: BindCraft binder design target Bet v1	two successful designs Count (designs with an observed binding signal (SPR), out of designs tested) count · higher Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Data 1 has one row per tested design with a Binding column holding 1, 0 or an empty cell. Treating the non-empty cells as the tested set reproduces the prose counts for BBF-14 (11 tested, 6 binding), Bet v1 (7, 2), CD45 (16, 4), Der f7 (10, 4), Der f21 (7, 4), IFNAR2 (9, 3), PD-1 (53, 13), SpCas9 (6, 6) and CLDN1 (7, 6), but not for PD-L1 (13 non-empty rows with 11 binding against 9 tested with 7 binding in the prose), CrSAS-6 (10 non-empty rows against 9 tested) or CbAgo (2 non-empty rows against 12 tested). The row filter is therefore ambiguous and no value is computed from these rows.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Results prose; Fig. 1b caption Fig. 1b's caption defines success as binding observed on SPR, but the PD-1 screen was BLI in a bivalent Fc-fusion format and the CLDN1 screen used soluble analogues. The 46.3% average therefore pools targets measured under different endpoints.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Fig. 1b caption; Results 'Binders targeting cell-surface receptors' and 'Targeting unexplored binding sites' Methods, coverage and source BindCraft binding screen against Bet v1 uc-binder-20261022-protocol-bindcraft-binding-screen Aggregation: Not reported One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Results 'Masking allergenic epitopes', paragraph 5: 'we identified two successful designs from seven tested binders against the birch allergen Bet v1 (Fig. 1b)'
Configuration: BindCraft default settings	Protocol: BindCraft per-target binding screen, hit where a binding signal was observed Dataset: BindCraft binder design target CD45	4 showed binding on SPR Count (designs with an observed binding signal (SPR), out of designs tested) count · higher Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Data 1 has one row per tested design with a Binding column holding 1, 0 or an empty cell. Treating the non-empty cells as the tested set reproduces the prose counts for BBF-14 (11 tested, 6 binding), Bet v1 (7, 2), CD45 (16, 4), Der f7 (10, 4), Der f21 (7, 4), IFNAR2 (9, 3), PD-1 (53, 13), SpCas9 (6, 6) and CLDN1 (7, 6), but not for PD-L1 (13 non-empty rows with 11 binding against 9 tested with 7 binding in the prose), CrSAS-6 (10 non-empty rows against 9 tested) or CbAgo (2 non-empty rows against 12 tested). The row filter is therefore ambiguous and no value is computed from these rows.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Results prose; Fig. 1b caption Fig. 1b's caption defines success as binding observed on SPR, but the PD-1 screen was BLI in a bivalent Fc-fusion format and the CLDN1 screen used soluble analogues. The 46.3% average therefore pools targets measured under different endpoints.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Fig. 1b caption; Results 'Binders targeting cell-surface receptors' and 'Targeting unexplored binding sites' Methods, coverage and source BindCraft binding screen against CD45 uc-binder-20261022-protocol-bindcraft-binding-screen Aggregation: Not reported One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Results 'Binders targeting cell-surface receptors', last paragraph: 'We tested 16 binders experimentally, out of which 4 showed binding on SPR (Fig. 1b)'
Configuration: BindCraft default settings	Protocol: BindCraft per-target binding screen, hit where a binding signal was observed Dataset: BindCraft binder design target Claudin1	all except binder17 to bind to sCLDN1-14 and sCLDN1-18 Count (designs with an observed binding signal (SPR prescreen at 10 micromolar against immobilised soluble claudin-1 analogues), out of designs tested) count · higher Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Data 1 has one row per tested design with a Binding column holding 1, 0 or an empty cell. Treating the non-empty cells as the tested set reproduces the prose counts for BBF-14 (11 tested, 6 binding), Bet v1 (7, 2), CD45 (16, 4), Der f7 (10, 4), Der f21 (7, 4), IFNAR2 (9, 3), PD-1 (53, 13), SpCas9 (6, 6) and CLDN1 (7, 6), but not for PD-L1 (13 non-empty rows with 11 binding against 9 tested with 7 binding in the prose), CrSAS-6 (10 non-empty rows against 9 tested) or CbAgo (2 non-empty rows against 12 tested). The row filter is therefore ambiguous and no value is computed from these rows.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Results prose; Fig. 1b caption Fig. 1b's caption defines success as binding observed on SPR, but the PD-1 screen was BLI in a bivalent Fc-fusion format and the CLDN1 screen used soluble analogues. The 46.3% average therefore pools targets measured under different endpoints.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Fig. 1b caption; Results 'Binders targeting cell-surface receptors' and 'Targeting unexplored binding sites' Methods, coverage and source BindCraft binding screen against Claudin1 uc-binder-20261022-protocol-bindcraft-binding-screen Aggregation: Not reported One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Results 'Targeting unexplored binding sites', paragraph 2: 'We tested seven binders and found all except binder17 to bind to sCLDN1-14 and sCLDN1-18 (Supplementary Fig. 4a)'
Configuration: BindCraft default settings	Protocol: BindCraft per-target binding screen, hit where a binding signal was observed Dataset: BindCraft binder design target Der f21	detect binding for four designs by SPR Count (designs with an observed binding signal (SPR), out of designs tested) count · higher Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Data 1 has one row per tested design with a Binding column holding 1, 0 or an empty cell. Treating the non-empty cells as the tested set reproduces the prose counts for BBF-14 (11 tested, 6 binding), Bet v1 (7, 2), CD45 (16, 4), Der f7 (10, 4), Der f21 (7, 4), IFNAR2 (9, 3), PD-1 (53, 13), SpCas9 (6, 6) and CLDN1 (7, 6), but not for PD-L1 (13 non-empty rows with 11 binding against 9 tested with 7 binding in the prose), CrSAS-6 (10 non-empty rows against 9 tested) or CbAgo (2 non-empty rows against 12 tested). The row filter is therefore ambiguous and no value is computed from these rows.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Results prose; Fig. 1b caption Fig. 1b's caption defines success as binding observed on SPR, but the PD-1 screen was BLI in a bivalent Fc-fusion format and the CLDN1 screen used soluble analogues. The 46.3% average therefore pools targets measured under different endpoints.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Fig. 1b caption; Results 'Binders targeting cell-surface receptors' and 'Targeting unexplored binding sites' Methods, coverage and source BindCraft binding screen against Der f21 uc-binder-20261022-protocol-bindcraft-binding-screen Aggregation: Not reported One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Results 'Masking allergenic epitopes', paragraph 4: 'we evaluated seven binders against Der f21 and could detect binding for four designs by SPR (Fig. 1b)'
Configuration: BindCraft default settings	Protocol: BindCraft per-target binding screen, hit where a binding signal was observed Dataset: BindCraft binder design target Der f7	identified 4 binders Count (designs with an observed binding signal (SPR), out of designs tested) count · higher Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Data 1 has one row per tested design with a Binding column holding 1, 0 or an empty cell. Treating the non-empty cells as the tested set reproduces the prose counts for BBF-14 (11 tested, 6 binding), Bet v1 (7, 2), CD45 (16, 4), Der f7 (10, 4), Der f21 (7, 4), IFNAR2 (9, 3), PD-1 (53, 13), SpCas9 (6, 6) and CLDN1 (7, 6), but not for PD-L1 (13 non-empty rows with 11 binding against 9 tested with 7 binding in the prose), CrSAS-6 (10 non-empty rows against 9 tested) or CbAgo (2 non-empty rows against 12 tested). The row filter is therefore ambiguous and no value is computed from these rows.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Results prose; Fig. 1b caption Fig. 1b's caption defines success as binding observed on SPR, but the PD-1 screen was BLI in a bivalent Fc-fusion format and the CLDN1 screen used soluble analogues. The 46.3% average therefore pools targets measured under different endpoints.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Fig. 1b caption; Results 'Binders targeting cell-surface receptors' and 'Targeting unexplored binding sites' Methods, coverage and source BindCraft binding screen against Der f7 uc-binder-20261022-protocol-bindcraft-binding-screen Aggregation: Not reported One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Results 'Masking allergenic epitopes', paragraph 2: 'We examined 10 designs against Der f7 experimentally and identified 4 binders (Fig. 1b)'
Configuration: BindCraft default settings	Protocol: BindCraft per-target binding screen, hit where a binding signal was observed Dataset: BindCraft binder design target IFNAR2	binding for three out of nine designs Count (designs with an observed binding signal (SPR), out of designs tested) count · higher Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Data 1 has one row per tested design with a Binding column holding 1, 0 or an empty cell. Treating the non-empty cells as the tested set reproduces the prose counts for BBF-14 (11 tested, 6 binding), Bet v1 (7, 2), CD45 (16, 4), Der f7 (10, 4), Der f21 (7, 4), IFNAR2 (9, 3), PD-1 (53, 13), SpCas9 (6, 6) and CLDN1 (7, 6), but not for PD-L1 (13 non-empty rows with 11 binding against 9 tested with 7 binding in the prose), CrSAS-6 (10 non-empty rows against 9 tested) or CbAgo (2 non-empty rows against 12 tested). The row filter is therefore ambiguous and no value is computed from these rows.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Results prose; Fig. 1b caption Fig. 1b's caption defines success as binding observed on SPR, but the PD-1 screen was BLI in a bivalent Fc-fusion format and the CLDN1 screen used soluble analogues. The 46.3% average therefore pools targets measured under different endpoints.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Fig. 1b caption; Results 'Binders targeting cell-surface receptors' and 'Targeting unexplored binding sites' Methods, coverage and source BindCraft binding screen against IFNAR2 uc-binder-20261022-protocol-bindcraft-binding-screen Aggregation: Not reported One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Results 'Binders targeting cell-surface receptors', paragraph 3: 'for IFNAR2 we could detect binding for three out of nine designs (Fig. 1b)'
Configuration: BindCraft default settings	Protocol: BindCraft per-target binding screen, hit where a binding signal was observed Dataset: BindCraft binder design target PD-1	a binding signal for 13 binders Count (designs with an observed binding signal (BLI, bivalent Fc-fusion format), out of designs tested) count · higher Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Data 1 has one row per tested design with a Binding column holding 1, 0 or an empty cell. Treating the non-empty cells as the tested set reproduces the prose counts for BBF-14 (11 tested, 6 binding), Bet v1 (7, 2), CD45 (16, 4), Der f7 (10, 4), Der f21 (7, 4), IFNAR2 (9, 3), PD-1 (53, 13), SpCas9 (6, 6) and CLDN1 (7, 6), but not for PD-L1 (13 non-empty rows with 11 binding against 9 tested with 7 binding in the prose), CrSAS-6 (10 non-empty rows against 9 tested) or CbAgo (2 non-empty rows against 12 tested). The row filter is therefore ambiguous and no value is computed from these rows.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Results prose; Fig. 1b caption Fig. 1b's caption defines success as binding observed on SPR, but the PD-1 screen was BLI in a bivalent Fc-fusion format and the CLDN1 screen used soluble analogues. The 46.3% average therefore pools targets measured under different endpoints.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Fig. 1b caption; Results 'Binders targeting cell-surface receptors' and 'Targeting unexplored binding sites' Methods, coverage and source BindCraft binding screen against PD-1 uc-binder-20261022-protocol-bindcraft-binding-screen Aggregation: Not reported One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Results 'Binders targeting cell-surface receptors', paragraph 1: 'We purified and screened 53 designs for binding using biolayer interferometry (BLI) in a bivalent Fc-fusion format. We observed a binding signal for 13 binders'
Configuration: BindCraft default settings	Protocol: BindCraft per-target binding screen, hit where a binding signal was observed Dataset: BindCraft binder design target PD-L1	seven showed a binding signal Count (designs with an observed binding signal (SPR prescreen at 10 micromolar against immobilised PD-L1-Fc, then SPR titration), out of designs tested) count · higher Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Data 1 has one row per tested design with a Binding column holding 1, 0 or an empty cell. Treating the non-empty cells as the tested set reproduces the prose counts for BBF-14 (11 tested, 6 binding), Bet v1 (7, 2), CD45 (16, 4), Der f7 (10, 4), Der f21 (7, 4), IFNAR2 (9, 3), PD-1 (53, 13), SpCas9 (6, 6) and CLDN1 (7, 6), but not for PD-L1 (13 non-empty rows with 11 binding against 9 tested with 7 binding in the prose), CrSAS-6 (10 non-empty rows against 9 tested) or CbAgo (2 non-empty rows against 12 tested). The row filter is therefore ambiguous and no value is computed from these rows.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Results prose; Fig. 1b caption Fig. 1b's caption defines success as binding observed on SPR, but the PD-1 screen was BLI in a bivalent Fc-fusion format and the CLDN1 screen used soluble analogues. The 46.3% average therefore pools targets measured under different endpoints.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Fig. 1b caption; Results 'Binders targeting cell-surface receptors' and 'Targeting unexplored binding sites' Methods, coverage and source BindCraft binding screen against PD-L1 uc-binder-20261022-protocol-bindcraft-binding-screen Aggregation: Not reported One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Results 'Binders targeting cell-surface receptors', paragraph 3: 'We tested nine designs against PD-L1 out of which seven showed a binding signal (Supplementary Fig. 3a)'
Configuration: BindCraft default settings	Protocol: BindCraft per-target binding screen, hit where a binding signal was observed Dataset: BindCraft binder design target SpCas9	All six tested binders bound the full-length apo SpCas9 enzyme Count (designs with an observed binding signal (SPR against full-length apo SpCas9), out of designs tested) count · higher Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Supplementary Data 1 has one row per tested design with a Binding column holding 1, 0 or an empty cell. Treating the non-empty cells as the tested set reproduces the prose counts for BBF-14 (11 tested, 6 binding), Bet v1 (7, 2), CD45 (16, 4), Der f7 (10, 4), Der f21 (7, 4), IFNAR2 (9, 3), PD-1 (53, 13), SpCas9 (6, 6) and CLDN1 (7, 6), but not for PD-L1 (13 non-empty rows with 11 binding against 9 tested with 7 binding in the prose), CrSAS-6 (10 non-empty rows against 9 tested) or CbAgo (2 non-empty rows against 12 tested). The row filter is therefore ambiguous and no value is computed from these rows.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Supplementary Data 1 (41586_2025_9429_MOESM4_ESM.csv), columns Target, DesignName, Binding; Results prose; Fig. 1b caption Fig. 1b's caption defines success as binding observed on SPR, but the PD-1 screen was BLI in a bivalent Fc-fusion format and the CLDN1 screen used soluble analogues. The 46.3% average therefore pools targets measured under different endpoints.One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Fig. 1b caption; Results 'Binders targeting cell-surface receptors' and 'Targeting unexplored binding sites' Methods, coverage and source BindCraft binding screen against SpCas9 uc-binder-20261022-protocol-bindcraft-binding-screen Aggregation: Not reported One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Results 'Modulating multi-domain nucleases', paragraph 2: 'All six tested binders bound the full-length apo SpCas9 enzyme (Supplementary Fig. 5a)'

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One-shot design of functional protein binders with BindCraft (Pacesa et al., Nature 2025) · Original source · Nature, version of record; Europe PMC JATS full text for PMC12507698

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Technical metadata and extraction receipts

Stable ID: uc-binder-20261022-protocol-bindcraft-binding-screen

areas: proteins-complexes; protein-structure
contexts: research
limitations: Developer-reported: the BindCraft authors built the pipeline, chose the targets and chose which designs to test.; The assay is not uniform across targets. Fig. 1b's caption says binding was observed on SPR, but PD-1 was screened by BLI in a bivalent Fc-fusion format and the claudin binders were prescreened against soluble analogues of the target rather than the wild-type protein.; No numeric binding threshold is stated. A successful design is one where a binding signal was observed.; Denominators are 6 to 53 designs per target, and the designs tested are about 10 of the top 20 ranked by the pipeline's own i_pTM filter, so design and selection are coupled.; No conventional comparator (directed evolution, display selection or grafting) was run on these targets.; No uncertainty is printed.; Two targets, CrSAS-6 and CbAgo, have a stated denominator but no stated numerator in the prose; their numerators appear only inside the Fig. 1b graphic, which was not read.
metric: count
metric direction: higher
metric qualifier: designs with an observed binding signal, out of designs tested
protocol: Designs passing the in silico filters are ranked by i_pTM, about ten of the top twenty are expressed and purified, and binding to the target is screened by SPR, or by BLI in a bivalent Fc-fusion format for PD-1, or by SPR against soluble analogues for claudin 1. Fig. 1b reports the number of designs with observed binding against the number tested.
review: artifact sha256: 74bd2902d46460ec387ed6ee46b5bf8fe61b9ea09f2d7be4daa2046ac7e59d5d; method: source-hash-verification; independent-cell-check; ai-assisted-source-review; method note: Re-downloaded from Europe PMC (HTTP 200, 226,059 bytes) and the SHA-256 recomputed and matched. Own flattening of the JATS XML; every quoted locator sentence and every printed value checked verbatim against it by a parser written for this review.; 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.ebi.ac.uk/europepmc/webservices/rest/PMC12507698/fullTextXML; reviewed at: 2026-10-22T15:00:00Z; reviewer: claude; reviewer note: Claude review agent, independent of the extraction agent; no human review claimed
selection: About 10 designs from the top 20 ranked by i_pTM.
selection bias: The ranking that chose the tested designs is the pipeline's own i_pTM score, so design and selection are not independent.
source locator: Fig. 1b caption; Results sections 'Binders targeting cell-surface receptors', 'Targeting unexplored binding sites', 'Masking allergenic epitopes' and 'Modulating multi-domain nucleases'
success threshold: criterion: a binding signal observed in the per-target screen; locator: Fig. 1b caption; note: No numeric affinity or signal threshold is stated, and the assay differs between targets.
unit: count
unit detail: designs
version: Nature 2025 version of record; Fig. 1b and the Results prose

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