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bioRxiv · 10.1101/2020.09.08.286302

MorphOT: Transport-based interpolation between EM maps with UCSF ChimeraX

Ecoffet, A.·Poitevin, F.·Dao Duc, K.
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Abstract

MotivationCryogenic Electron-Microscopy offers the unique potential to capture conformational heterogeneity, by solving multiple 3D classes that co-exist within a single cryo-EM image dataset. To investigate the extent and implications of such heterogeneity, we propose to use an optimal-transport based metric to interpolate barycenters between EM maps and produce morphing trajectories. While standard linear interpolation mostly fails to produce realistic transitions, our method yields continuous trajectories that displace densities to morph one map into the other, instead of blending them. ImplementationOur method is implemented as a plug-in for ChimeraX called MorphOT, which allows the use of both CPU or GPU resources. The code is publicly available on GitHub (https://github.com/kdd-ubc/MorphOT.git), with documentation containing tutorial and datasets. Contactkdd@math.ubc.ca

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Ecoffet, A., Poitevin, F., Dao Duc, K.. 2020-09-09. MorphOT: Transport-based interpolation between EM maps with UCSF ChimeraX. https://doi.org/10.1101/2020.09.08.286302

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