ReQFlow: Rectified Quaternion Flow for Efficient and High-Quality
  Protein Backbone Generation
Authors: name: Angxiao Yue; name: Zichong Wang; name: Hongteng Xu
Published: 2025-02-20 15:20:37

Abstract: Protein backbone generation plays a central role in de novo protein design
and is significant for many biological and medical applications. Although
diffusion and flow-based generative models provide potential solutions to this
challenging task, they often generate proteins with undesired designability and
suffer computational inefficiency. In this study, we propose a novel rectified
quaternion flow (ReQFlow) matching method for fast and high-quality protein
backbone generation. In particular, our method generates a local translation
and a 3D rotation from random noise for each residue in a protein chain, which
represents each 3D rotation as a unit quaternion and constructs its flow by
spherical linear interpolation (SLERP) in an exponential format. We train the
model by quaternion flow (QFlow) matching with guaranteed numerical stability
and rectify the QFlow model to accelerate its inference and improve the
designability of generated protein backbones, leading to the proposed ReQFlow
model. Experiments show that ReQFlow achieves state-of-the-art performance in
protein backbone generation while requiring much fewer sampling steps and
significantly less inference time (e.g., being 37x faster than RFDiffusion and
62x faster than Genie2 when generating a backbone of length 300), demonstrating
its effectiveness and efficiency. The code is available at
https://github.com/AngxiaoYue/ReQFlow.