P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching

• URL: http://arxiv.org/abs/2411.17196v1
• Date: Tue, 26 Nov 2024 08:10:12 GMT
• Title: P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching
• Authors: Yaowei Jin, Qi Huang, Ziyang Song, Mingyue Zheng, Dan Teng, Qian Shi,
• Abstract summary: P2DFlow is a generative model based on SE(3) flow matching to predict the structural ensembles of proteins. When trained and evaluated on MD datasets of ATLAS, P2DFlow outperforms other baseline models. As a potential proxy agent for protein molecular simulation, the high-quality ensembles generated by P2DFlow could significantly aid in understanding protein functions across various scenarios.
• Score: 8.620021796568087
• License:
• Abstract: Biological processes, functions, and properties are intricately linked to the ensemble of protein conformations, rather than being solely determined by a single stable conformation. In this study, we have developed P2DFlow, a generative model based on SE(3) flow matching, to predict the structural ensembles of proteins. We specifically designed a valuable prior for the flow process and enhanced the model's ability to distinguish each intermediate state by incorporating an additional dimension to describe the ensemble data, which can reflect the physical laws governing the distribution of ensembles, so that the prior knowledge can effectively guide the generation process. When trained and evaluated on the MD datasets of ATLAS, P2DFlow outperforms other baseline models on extensive experiments, successfully capturing the observable dynamic fluctuations as evidenced in crystal structure and MD simulations. As a potential proxy agent for protein molecular simulation, the high-quality ensembles generated by P2DFlow could significantly aid in understanding protein functions across various scenarios. Code is available at https://github.com/BLEACH366/P2DFlow.

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