AlphaFold3, 200 models per target, top model picked by AlphaFold3 pTM (Fromm et al. 2026)
AlphaFold3, 200 models per target, top model picked by AlphaFold3 pTM: 40 seeds (1 to 40) x 5 diffusion samples; MSAs from the AlphaFold 2.3.2 pipeline (commit f251de6), bfd_uniref_hits.a3m.
Overview
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Evaluations and results
1 evaluation · 3 results. Different protocols are not a single leaderboard.
Protocol: Picking the top AlphaFold3 model per antibody-antigen target with a confidence score · Dataset: Fromm et al. 2026 antibody-antigen benchmark: 110 complexes released after 30 September 2021
Sorted by DockQ (mean over targets of the DockQ of the model picked by this score) (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 | DockQ (mean over targets of the DockQ of the model picked by this score) | Spearman (mean over targets of the per-target correlation of score against DockQ) | Spearman (score against DockQ over all models of all targets) |
|---|---|---|---|
| AlphaFold3, 200 models per target, top model picked by AlphaFold3 pTM (Fromm et al. 2026)Evaluation | 0.369 | 0.2 | 0.67 |
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Evidence
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Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record and release history
- Evaluating deep learning based structure prediction methods on antibody-antigen complexes · Original source · Bioinformatics 42(4):btag136, 2026; PMC13061134 full-text XML
Technical metadata and extraction receipts
Stable ID: structural-20261009-config-fromm2026-af3-ptm
- areas
- proteins-complexes
- contexts
- research
- method types
- foundation_model
- reported name
- pTM
- foundation model eligible
- true
- source locator
- Table 1, row 'pTM'; sections 2.2.2 and 2.7
- missing metadata
- version: reason: unreported; note: No release or commit is printed for this run
- samples
- 200
- parameters
- 40 seeds (1 to 40) x 5 diffusion samples; MSAs from the AlphaFold 2.3.2 pipeline (commit f251de6), bfd_uniref_hits.a3m
- selection
- Model with the highest pTM among the 200
- provenance note
- Configuration as run in the cited comparison.
Related records
- configuration of: AlphaFold 3
- system: AlphaFold3 top model by pTM on 110 post-cutoff antibody-antigen complexes (Fromm et al. 2026)