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Boltz-2 (Probability) as a screening score

Ranks a compound library by the classification output of Boltz-2's affinity prediction module taken from the predicted protein-ligand complex.

1 evaluation · 10 results

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Evaluations and results

1 evaluation · 10 results. Different protocols are not a single leaderboard.

Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) · Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025

Sorted by AUROC (AUROC, mean over the 79 DEKOIS 2.0 targets) (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	AUROC (AUROC, mean over the 79 DEKOIS 2.0 targets)	AUROC (AUROC, median over the 79 DEKOIS 2.0 targets)	Bedroc (BEDROC with alpha = 80.5, mean over the 79 DEKOIS 2.0 targets)	Bedroc (BEDROC with alpha = 80.5, median over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 0.5% of the ranked library, mean over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 0.5% of the ranked library, median over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 1% of the ranked library, mean over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 1% of the ranked library, median over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 5% of the ranked library, mean over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 5% of the ranked library, median over the 79 DEKOIS 2.0 targets)
Boltz-2 (Probability) as a screening scoreEvaluation	0.911	0.964	0.82	0.925	26.7	31	25.8	28.6	14.3	16

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Boltz-2 (Probability) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.911 AUROC (AUROC, mean over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 (Probability) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Boltz-2 (Probability)a', column 'AUROC' (Mean)
Configuration: Boltz-2 (Probability) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.964 AUROC (AUROC, median over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 (Probability) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Boltz-2 (Probability)a', column 'AUROC' (Med)
Configuration: Boltz-2 (Probability) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.82 Bedroc (BEDROC with alpha = 80.5, mean over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 (Probability) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Boltz-2 (Probability)a', column 'BEDROC (α = 80.5)' (Mean)
Configuration: Boltz-2 (Probability) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.925 Bedroc (BEDROC with alpha = 80.5, median over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 (Probability) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Boltz-2 (Probability)a', column 'BEDROC (α = 80.5)' (Med)
Configuration: Boltz-2 (Probability) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	26.7 Enrichment factor (EF at the top 0.5% of the ranked library, mean over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 (Probability) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Boltz-2 (Probability)a', column 'EF0.5%' (Mean)
Configuration: Boltz-2 (Probability) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	31 Enrichment factor (EF at the top 0.5% of the ranked library, median over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 (Probability) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Boltz-2 (Probability)a', column 'EF0.5%' (Med)
Configuration: Boltz-2 (Probability) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	25.8 Enrichment factor (EF at the top 1% of the ranked library, mean over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 (Probability) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Boltz-2 (Probability)a', column 'EF1%' (Mean)
Configuration: Boltz-2 (Probability) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	28.6 Enrichment factor (EF at the top 1% of the ranked library, median over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 (Probability) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Boltz-2 (Probability)a', column 'EF1%' (Med)
Configuration: Boltz-2 (Probability) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	14.3 Enrichment factor (EF at the top 5% of the ranked library, mean over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 (Probability) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Boltz-2 (Probability)a', column 'EF5%' (Mean)
Configuration: Boltz-2 (Probability) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	16 Enrichment factor (EF at the top 5% of the ranked library, median over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 (Probability) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'Boltz-2 (Probability)a', column 'EF5%' (Med)

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Shen et al. 2025, Chemical Science (Europe PMC full text) · Original source · PMC12704515 (Chem Sci, published 2025-12-11)

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Technical metadata and extraction receipts

Stable ID: hitdisc-20261022-config-boltz2-probability

areas: molecular-interactions
contexts: research
method types: foundation_model
reported name: Boltz-2 (Probability)
configuration type: paper_evaluation
foundation model eligible: true
review: method: scope-review; automated-source-review; reviewer: claude; reviewer note: Claude review agent, independent of the extraction agent; no human review claimed; date: 2026-10-22; method note: Read the record against the pinned sources and against docs/use-cases.md and docs/record-contract.md.; note: Record checked against the pinned source and the record contract. Transcription checked; not reproduced and not reviewed by a human scientist.; artifact sha256: 11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12704515/fullTextXML; receipt: data/omics/use-case-coverage-hitdisc-20261022/review.json
version: Boltz-2 version 2.0.0, the recommended single model with random seed 1, MMseqs2 web-service MSAs
access reuse: Source code at https://github.com/google-deepmind/alphafold3, https://github.com/bytedance/Protenix and https://github.com/jwohlwend/boltz (Data availability); no licence is stated in the source
parameters: All parameters other than the sample count and seed left at default or recommended values
score training overlap: The authors state that the Boltz-2 affinity module's training data, drawn from public binding databases including PubChem, ChEMBL and BindingDB, may overlap substantially with the test samples, so these results are reported for completeness and excluded from the authors' primary comparison.
source locator: Methods 'Complex structure prediction' and 'Scoring schemes'

Related records

configuration of: Boltz-2
system: Boltz-2 (Probability) on DEKOIS 2.0 (Shen et al. 2025 Table 1)

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