Learning Universal Representations of Intermolecular Interactions with ATOMICA

Molecular interactions underlie nearly all biological processes, yet most representation models describe isolated entities or specialize in a single molecular setting. Here, we introduce ATOMICA, an interaction-centered geometric deep learning model designed to learn transferable representations of intermolecular interfaces across proteins, small molecules, metal ions, and nucleic acids. Self-supervised pretraining on 2,037,972 interaction complexes yields representations spanning atoms, molecular building blocks, and complete interfaces. The latent space captures molecular identity and interaction context, supporting sequence recovery and zero-shot prioritization of residues involved in non-covalent interactions. ATOMICA provides structural information complementary to sequence representations on RNA and protein-pocket ligand classification. Across protein-pocket analyses, ATOMICA distinguishes ATP- and ADP-associated pocket states and retrieves ligand-matched pockets across proteins without detectable structural alignment. The latent space also enables cross-modal comparison, with orthosteric inhibitor embeddings retrieving regions proximal to native peptide and protein interfaces. Applied to the dark proteome, ATOMICA-Ligand predicts candidate ions or cofactors for 2,646 pockets, and five heme candidates show Soret-band shifts consistent with heme association. Together, these results show how interaction-centered molecular representations can transfer structural information across molecular interaction types and generate experimentally testable hypotheses.