A Systematic Evaluation of Co-folding Model Representations for Small-Molecule Learning

ArXi:2602.13249v2 Announce Type: replace-cross Small-molecule foundation models are typically pretrained on standalone molecular data, unlike vision and language models that often benefit from cross-modal or relational supervision. Protein-ligand co-folding provides a molecular analogue of such supervision by exposing models to atom-level ligand-protein interactions, raising the question of whether co-folding models can yield strong small-molecule representations.