SE(3) diffusion model with application to protein backbone generation

The design of novel protein structures remains a challenge in protein engineering for applications across biomedicine and chemistry. In this line of work, a diffusion model over rigid bodies in 3D (referred to as frames) has shown success in generating novel, functional protein backbones that have n...

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Bibliographic Details
Published in:arXiv.org 2023-05
Main Authors: Yim, Jason, Trippe, Brian L, De Bortoli, Valentin, Mathieu, Emile, Doucet, Arnaud, Barzilay, Regina, Jaakkola, Tommi
Format: Article
Language:English
Subjects:
Amino acids
Diffusion
Frames
Monomers
Proteins
Rigid structures
Online Access:Get full text
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Summary:The design of novel protein structures remains a challenge in protein engineering for applications across biomedicine and chemistry. In this line of work, a diffusion model over rigid bodies in 3D (referred to as frames) has shown success in generating novel, functional protein backbones that have not been observed in nature. However, there exists no principled methodological framework for diffusion on SE(3), the space of orientation preserving rigid motions in R3, that operates on frames and confers the group invariance. We address these shortcomings by developing theoretical foundations of SE(3) invariant diffusion models on multiple frames followed by a novel framework, FrameDiff, for learning the SE(3) equivariant score over multiple frames. We apply FrameDiff on monomer backbone generation and find it can generate designable monomers up to 500 amino acids without relying on a pretrained protein structure prediction network that has been integral to previous methods. We find our samples are capable of generalizing beyond any known protein structure.
ISSN:2331-8422