AlphaFold3 3.0.1, 50 diffusion samples, seed 1, built-in data pipeline (Smorodina et al. 2026)
AlphaFold3 3.0.1, 50 diffusion samples, seed 1, built-in data pipeline: num_diffusion_samples = 50; run_data_pipeline = true; seed = 1; MSAs from the built-in pipeline.
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Evaluations and results
3 evaluations · 8 results. Different protocols are not a single leaderboard.
Sorted by Average precision (cognate against shuffled pairs ranked by ipTM) (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 | Average precision (cognate against shuffled pairs ranked by ipTM) | DockQ (median over complexes of the best DockQ among N = 1 samples) | DockQ (median over complexes of the best DockQ among N = 100 samples) | Pearson (change in ipTM against change in DockQ under saturation sampling) | Pearson (ipTM against DockQ for the best-DockQ sample of each complex) | Pearson (ipTM against DockQ for the first sample (sample0) of each complex) | Proportion (share of predictions with ipTM at least 0.5 and DockQ below 0.23 (confident failures, Q2)) | Proportion (share of predictions with ipTM below 0.5 and DockQ at least 0.23 (unconfident successes, Q4)) |
|---|---|---|---|---|---|---|---|---|---|
| AlphaFold3 3.0.1, 50 diffusion samples, seed 1, built-in data pipeline (Smorodina et al. 2026)Evaluation | Telling cognate from shuffled nanobody-antigen pairs by ipTM, Smorodina et al. 2026 all-against-all VHH-antigen pairing matrix (91 unique PDB entries) | 0.187 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1, 50 diffusion samples, seed 1, built-in data pipeline (Smorodina et al. 2026)Evaluation | Best DockQ against sampling depth on cognate nanobody-antigen complexes, Smorodina et al. 2026 nanobody-antigen benchmark: 106 cognate VHH-antigen complexes | Not reported | 0.24 | 0.68 | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold3 3.0.1, 50 diffusion samples, seed 1, built-in data pipeline (Smorodina et al. 2026)Evaluation | How well ipTM tracks DockQ on cognate nanobody-antigen complexes, Smorodina et al. 2026 nanobody-antigen benchmark: 106 cognate VHH-antigen complexes | Not reported | Not reported | Not reported | -0.027 | 0.736 | 0.888 | 2% | 28% |
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Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record and release history
- Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores · Original source · bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed
Technical metadata and extraction receipts
Stable ID: structural-20261009-config-smorodina2026-af3
- areas
- proteins-complexes
- contexts
- research
- method types
- foundation_model
- reported name
- AF3
- foundation model eligible
- true
- source locator
- Methods, structure prediction (P75)
- version
- alphafold3-3.0.1
- parameters
- num_diffusion_samples = 50; run_data_pipeline = true; seed = 1; MSAs from the built-in pipeline
- training overlap
- 30 of 106 cognate systems in the training set; 76 not (AF3 cutoff about 30 September 2021)
- provenance note
- Configuration as run in the cited comparison.
Related records
- configuration of: AlphaFold 3
- system: AF3 on Telling cognate from shuffled nanobody-antigen pairs by ipTM (Smorodina et al. 2026)
- system: AF3 on Best DockQ against sampling depth on cognate nanobody-antigen complexes (Smorodina et al. 2026)
- system: AF3 on How well ipTM tracks DockQ on cognate nanobody-antigen complexes (Smorodina et al. 2026)