Ophiuchus: Scalable Modeling of Protein Structures through Hierarchical Coarse-graining SO(3)-Equivariant Autoencoders

Allan Dos Santos Costa, Ilan Mitnikov, Mario Geiger, Manvitha Ponnapati, Tess Smidt, JOSEPH JACOBSON

Track: Machine learning: computational method and/or computational results

Keywords: Protein Representation learning, autoencoder, SO(3)-equivariant networks, unsupervised learning, diffusion, latent diffusion

Abstract: Three-dimensional native states of natural proteins display recurring and hierarchical patterns. Yet, traditional graph-based modeling of protein structures is often limited to operate within a single fine-grained resolution, and lacks hourglass neural architectures to learn those high-level building blocks. We narrow this gap by introducing Ophiuchus, an SO(3)-equivariant coarse-graining model that efficiently operates on all-atom protein structures. Our model departs from current approaches that employ graph modeling, instead focusing on local convolutional coarsening to model sequence-motif interactions with efficient time complexity in protein length. We measure the reconstruction capabilities of Ophiuchus across different compression rates, and compare it to existing models. We examine the learned latent space and demonstrate its utility through conformational interpolation. Finally, we leverage denoising diffusion probabilistic models (DDPM) in the latent space to efficiently sample protein structures. Our experiments demonstrate Ophiuchus to be a scalable basis for efficient protein modeling and generation.

Submission Number: 103