WikiSysop: Created page with "== Citation == A. T. Riahi, G. Woollard, F. Poitevin, A. Condon, and K. D. Duc, “Alignot: An optimal transport based algorithm for fast 3d alignment with applications to cryogenic electron microscopy density maps,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023. == Abstract == Aligning electron density maps from Cryogenic electron microscopy (cryo-EM) is a first key step for studying multiple conformations of a biomolecule. As this step re..."

2024-12-27T07:37:00Z

Created page with "== Citation == A. T. Riahi, G. Woollard, F. Poitevin, A. Condon, and K. D. Duc, “Alignot: An optimal transport based algorithm for fast 3d alignment with applications to cryogenic electron microscopy density maps,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023. == Abstract == Aligning electron density maps from Cryogenic electron microscopy (cryo-EM) is a first key step for studying multiple conformations of a biomolecule. As this step re..."

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== Citation ==

A. T. Riahi, G. Woollard, F. Poitevin, A. Condon, and K. D. Duc, “Alignot: An optimal transport based algorithm for fast 3d alignment with applications to cryogenic electron microscopy density maps,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023.

== Abstract ==

Aligning electron density maps from Cryogenic electron microscopy (cryo-EM) is a first key step for studying multiple
conformations of a biomolecule. As this step remains costly and challenging, with standard alignment tools being potentially stuck in
local minima, we propose here a new procedure, called AlignOT, which relies on the use of computational optimal transport (OT) to
align EM maps in 3D space. By embedding a fast estimation of OT maps within a stochastic gradient descent algorithm, our method
searches for a rotation that minimizes the Wasserstein distance between two maps, represented as point clouds. We quantify the
impact of various parameters on the precision and accuracy of the alignment, and show that AlignOT can outperform the standard
local alignment methods, with an increased range of rotation angles leading to proper alignment. We further benchmark AlignOT on
various pairs of experimental maps, which account for different types of conformational heterogeneities and geometric properties. As
our experiments show good performance, we anticipate that our method can be broadly applied to align 3D EM maps.

== Keywords ==

== Links ==

https://ieeexplore.ieee.org/abstract/document/10298813

== Related software ==

== Related methods ==

== Comments ==

2023Riahi Transport - Revision history