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OPUS-DSD: deep structural disentanglement for cryo-EM single-particle analysis.
- Source :
-
Nature methods [Nat Methods] 2023 Nov; Vol. 20 (11), pp. 1729-1738. Date of Electronic Publication: 2023 Oct 09. - Publication Year :
- 2023
-
Abstract
- Cryo-electron microscopy (cryo-EM) captures snapshots of dynamic macromolecules, collectively illustrating the involved structural landscapes. This provides an exciting opportunity to explore the structural variations of macromolecules under study. However, traditional cryo-EM single-particle analysis often yields static structures. Here we describe OPUS-DSD, an algorithm capable of efficiently reconstructing the structural landscape embedded in cryo-EM data. OPUS-DSD uses a three-dimensional convolutional encoder-decoder architecture trained with cryo-EM images, thereby encoding structural variations into a smooth and easily analyzable low-dimension space. This space can be traversed to reconstruct continuous dynamics or clustered to identify distinct conformations. OPUS-DSD can offer meaningful insights into the structural variations of macromolecules, filling in the gaps left by traditional cryo-EM structural determination, and potentially improves the reconstruction resolution by reliably clustering similar particles within the dataset. These functionalities are especially relevant to the study of highly dynamic biological systems. OPUS-DSD is available at https://github.com/alncat/opusDSD .<br /> (© 2023. The Author(s).)
Details
- Language :
- English
- ISSN :
- 1548-7105
- Volume :
- 20
- Issue :
- 11
- Database :
- MEDLINE
- Journal :
- Nature methods
- Publication Type :
- Academic Journal
- Accession number :
- 37813988
- Full Text :
- https://doi.org/10.1038/s41592-023-02031-6