How do Co-Folding Models Organize Structural Information?
- 1Department of Chemistry, KAIST
Abstract
Co-folding models accurately predict biomolecular complexes, but how their internal representations support joint structure prediction remains unclear. We analyze the Boltz-1 trunk by decomposing its pair representation into intra-chain and inter-chain blocks and applying ablation, layer-wise representation geometry, and activation patching. Our results show that structural information is distributed across three streams: the single representation carries token-internal atomic detail, the intra-chain pair representation encodes chain-level geometry, and the inter-chain pair representation controls relative molecular arrangement. Across the trunk depth, representations follow a Mix-Compress-Refine trajectory, while linear probes reveal that intra-chain distance content is largely supplied by MSA preconditioning and inter-chain distance content is constructed progressively across Pairformer layers at each recycle. Apo-holo patching further shows that ligand-induced backbone changes are not fully resolved before diffusion; instead, the diffusion module reconciles partially inconsistent intra- and inter-chain constraints. These findings provide a mechanistic view of how co-folding trunks organize structural information and suggest more partition-aware designs for future biomolecular structure prediction models.
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BibTeX
@misc{park2026cofolding,
title = {{How do Co-Folding Models Organize Structural Information?}},
author = {M. Park and S. Kim and S. Moon and H. Kim and G. Jeon and W. Y. Kim},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.06.749739},
url = {https://www.biorxiv.org/content/10.64898/2026.09.06.749739v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - How do Co-Folding Models Organize Structural Information?
AU - M. Park
AU - S. Kim
AU - S. Moon
AU - H. Kim
AU - G. Jeon
AU - W. Y. Kim
PY - 2026
DA - 2026/09/06
PB - bioRxiv
DO - 10.64898/2026.09.06.749739
UR - https://www.biorxiv.org/content/10.64898/2026.09.06.749739v1
AB - Co-folding models accurately predict biomolecular complexes, but how their internal representations support joint structure prediction remains unclear. We analyze the Boltz-1 trunk by decomposing its pair representation into intra-chain and inter-chain blocks and applying ablation, layer-wise representation geometry, and activation patching. Our results show that structural information is distributed across three streams: the single representation carries token-internal atomic detail, the intra-chain pair representation encodes chain-level geometry, and the inter-chain pair representation controls relative molecular arrangement. Across the trunk depth, representations follow a Mix-Compress-Refine trajectory, while linear probes reveal that intra-chain distance content is largely supplied by MSA preconditioning and inter-chain distance content is constructed progressively across Pairformer layers at each recycle. Apo-holo patching further shows that ligand-induced backbone changes are not fully resolved before diffusion; instead, the diffusion module reconciles partially inconsistent intra- and inter-chain constraints. These findings provide a mechanistic view of how co-folding trunks organize structural information and suggest more partition-aware designs for future biomolecular structure prediction models.
ER -