Joint Discrete and SE(3) Diffusion for Protein Interface Design

Abstract

The design of high-affinity, target-specific protein binders is central to the development of modern therapeutics. However, existing protein-generation methods remain limited in this setting, as many generated designs fail to simultaneously achieve geometric and physicochemical complementarity at binding interfaces. To address this challenge, we introduce PIDiff, a physicochemically enhanced multimodal diffusion framework for protein-protein complex design. PIDiff jointly designs target-conditioned protein sequences and structures by coupling diffusion in discrete sequence space with diffusion on the continuous (SE(3)) structural manifold. At its core, PIDiff employs PIFormer, a novel architecture that interleaves geometry-aware invariant point attention with global sequence self-attention. We further curate PIBench, a protein-protein complex dataset with diverse target scaffolds derived from the Protein Data Bank (PDB). We first pretrain PIDiff on PIBench and subsequently fine-tune it for two therapeutically relevant applications: minibinder design and antibody design. PPFrame consistently outperforms baseline methods across sequence design success rate, structure binding energy, and sequence-structure co-designability on all tasks.