Author

Minjae Park

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Open access Jul 2026

Benchmarking AlphaFold and related deep learning approaches for modeling antibody and TCR antigen recognition

It is shown that increased sampling and AlphaFold3 generally improve performance relative to default sampling and AlphaFold2, however predictive accuracy and improvement levels varied considerably among interface classes, with antibody-peptide complexes representing a challenge despite their small antigen size.

Rui Yin, S. Saravanakumar, S. Shi et al. · bioRxiv · 1 citation

Open access Aug 2026

Benchmarking antibody-antigen co-folding on human monomeric antigens

The most recent methods substantially outperformed earlier ones, producing medium-or-better top-ranked models for approximately half of post-cutoff Fv complexes without templates or experimental restraints, and performing similarly on antigens with or without a close pre-cutoff homolog.

Minjae Park, Roman Nett, Brian M. Petersen et al. · bioRxiv · 0 citations