English

Non-Canonical Crosslinks Confound Evolutionary Protein Structure Models

Biomolecules 2025-03-25 v1 Artificial Intelligence

Abstract

Evolution-based protein structure prediction models have achieved breakthrough success in recent years. However, they struggle to generalize beyond evolutionary priors and on sequences lacking rich homologous data. Here we present a novel, out-of-domain benchmark based on sactipeptides, a rare class of ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by sulfur-to-α\alpha-carbon thioether bridges creating cross-links between cysteine residues and backbone. We evaluate recent models on predicting conformations compatible with these cross-links bridges for the 10 known sactipeptides with elucidated post-translational modifications. Crucially, the structures of 5 of them have not yet been experimentally resolved. This makes the task a challenging problem for evolution-based models, which we find exhibit limited performance (0.0% to 19.2% GDT-TS on sulfur-to-α\alpha-carbon distance). Our results point at the need for physics-informed models to sustain progress in biomolecular structure prediction.

Keywords

Cite

@article{arxiv.2503.17368,
  title  = {Non-Canonical Crosslinks Confound Evolutionary Protein Structure Models},
  author = {Romain Lacombe},
  journal= {arXiv preprint arXiv:2503.17368},
  year   = {2025}
}
R2 v1 2026-06-28T22:30:09.854Z