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Quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories

Updated: Nov 22, 2022

Published in Bioinformatics

Mallet V, Nilges M, Bouvier G

Summary: We implemented the Self-Organizing Maps algorithm running efficiently on GPUs, and also provide several clustering methods of the resulting maps. We provide scripts and a use case to cluster macro-molecular conformations generated by molecular dynamics simulations. Availability and implementation: The method is available on GitHub and distributed as a pip package. More info at:

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