Joint Discrete and SE(3) Diffusion for Protein Interface Design
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 arc...
| Authors | Zhenqiao Song, Jianwen Xie, Lei Li |
|---|---|
| Primary category | cs.AI |
| Published | 10 October 2026 |
| Last updated at source | 10 October 2026 |
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