ProteinAE: Protein Diffusion Autoencoders for Structure Encoding

Shaoning Li, Le Zhuo, Yusong Wang, Mingyu Li, Xinheng He, Fandi Wu, Hongsheng Li, Pheng-Ann Heng

Keywords: Protein Auto-encoder; Protein Structure modeling

Abstract: Developing effective representations of protein structures is essential for advancing protein science, particularly for protein generative modeling. Current approaches often grapple with the complexities of the $\operatorname{SE}(3)$ manifold, rely on discrete tokenization, or the need for multiple training objectives, all of which can hinder the model optimization and generalization. We introduce ProteinAE, a novel and streamlined protein diffusion autoencoder designed to overcome these challenges by directly mapping protein backbone coordinates from $\operatorname{E}(3)$ into a continuous, compact latent space. ProteinAE employs a non-equivariant Diffusion Transformer with a bottleneck design for efficient compression and is trained end-to-end with a single flow matching objective, substantially simplifying the optimization pipeline. We demonstrate that ProteinAE achieves state-of-the-art reconstruction quality, outperforming existing autoencoders. The resulting latent space serves as a powerful foundation for a latent diffusion model that bypasses the need for explicit equivariance. This enables efficient, high-quality structure generation that is competitive with leading structure-based approaches and significantly outperforms prior latent-based methods. Code is available at https://github.com/OnlyLoveKFC/ProteinAE_v1.

Primary Area: applications to physical sciences (physics, chemistry, biology, etc.)

Submission Number: 11944