Towards Generalizing Pretrained All-Atom Representations to Unified Binder Design

arXiv:2610.37994v1 Announce Type: new Abstract: PairFormer-based all-atom models demonstrate strong capabilities in biomolecular binder design. However, existing methods often use all-atom representations for modality-specific binder design, such as protein and peptide design. In contrast, recent geometric latent diffusion models pursue unified binder design by representing molecular blocks from different modalities in a shared latent space. These complementary strengths motivate us to investigate how to generalize the use of pretrained all-atom representations to unified binder design. We introduce PairFuse, a parameter-efficient method that enables this generalization through representation fusion.