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Alignment of Partially Overlapping Cryo-EM Maps Using Unbalanced Gromov-Wasserstein Divergence
Open accessPublished version of a preprint
Abstract
Aligning EM density maps and fitting atomic models are essential steps in single-particle cryogenic electron microscopy (cryo-em), with recent methods leveraging various algorithms and machine learning tools. As aligning maps remains challenging in the presence of a map that only partially fits the other (e.g., one subunit), we here propose a procedure, em partial alignment with optimal transport (EMPOT), for partial alignment of three-dimensional (3D) maps. EMPOT finds a coupling between 3D point-cloud representations, which is associated with their so-called unbalanced Gromov Wasserstein divergence, and uses this coupling to find an optimal rigid body transformation. On running and benchmarking our method with experimental maps and structures, we show that EMPOT outperforms standard methods for aligning density maps and fitting atomic models to a density map, suggesting potential applications of partial optimal transport for improving cryo-em pipelines.
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Metadata
- Authors
- Tajmir Riahi, A., Zhang, C., Condon, A., Chen, J., & Dao Duc, K.
- Affiliations
- University of British Columbia
- University of British Columbia (CA)
- Amgen (Canada) (CA)
- Venue
- PRX Life
- Publisher
- American Physical Society (APS)
- Published
- 2025-04-29
- Volume
- 3
- Issue
- 2
- ISSN
- 2835-8279 (ISSN-L)
- OpenAlex
- W4409922039
- Cited by
- 5
- References
- 1
- Citations by year
- 2026: 1 · 2025: 3
- FWCI
- 1.45
- Type
- journal article
- Language
- en
- Open access
- diamond
- doi.org
- Licence
- Locations
- PRX Life (publishedVersion, cc-by)
- arXiv (Cornell University) (submittedVersion, cc-by)
- arXiv (Cornell University) (cc-by)
- Funders
- University of British Columbia (IT12184)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- partial alignment, optimal transport, rigid transformation, single-particle cryo-electron microscopy, 3D density maps
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