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arXiv · 2410.08631

CryoFM: A Flow-based Foundation Model for Cryo-EM Densities

Yi Zhou·Yilai Li·Jing Yuan·Quanquan Gu
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Abstract

Cryo-electron microscopy (cryo-EM) is a powerful technique in structural biology and drug discovery, enabling the study of biomolecules at high resolution. Significant advancements by structural biologists using cryo-EM have led to the production of over 38,626 protein density maps at various resolutions1. However, cryo-EM data processing algorithms have yet to fully benefit from our knowledge of biomolecular density maps, with only a few recent models being data-driven but limited to specific tasks. In this study, we present CryoFM, a foundation model designed as a generative model, learning the distribution of high-quality density maps and generalizing effectively to downstream tasks. Built on flow matching, CryoFM is trained to accurately capture the prior distribution of biomolecular density maps. Furthermore, we introduce a flow posterior sampling method that leverages CRYOFM as a flexible prior for several downstream tasks in cryo-EM and cryo-electron tomography (cryo-ET) without the need for fine-tuning, achieving state-of-the-art performance on most tasks and demonstrating its potential as a foundational model for broader applications in these fields.

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Yi Zhou, Yilai Li, Jing Yuan, Quanquan Gu. 2024-10-11. CryoFM: A Flow-based Foundation Model for Cryo-EM Densities. https://arxiv.org/abs/2410.08631

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