BindFM: Universal Biomolecular Binding Foundation Model

BindFM is a from-scratch SE(3)-equivariant foundation model for universal biomolecular binding prediction across five modalities: protein–small molecule, protein–protein, protein–nucleic acid, nucleic–small molecule, and nucleic–nucleic. Built with a shared atom-level EGNN encoder and PairFormer trunk, co-trained on binding affinity, 3D complex structure, and de novo binder generation. Special emphasis on therapeutic aptamers including LNA, 2'F, 2'OMe, and phosphorothioate modifications.