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. 2023 Sep 18;24(18):14245. doi: 10.3390/ijms241814245

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© 2023 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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Illustrative workflow using Flexibility Hub and Scipion-EM-ProDy to solve challenges with interpreting landscapes from continuous heterogeneity analysis of single particle images and obtaining reasonable structures. There are 4 main parts. (1) A general Flexibility Hub starts from a set of particles from traditional SPA; (2) A fast, flexible fitting pipeline based on Zernike3D creates several structures; (3) ProDy ensemble analysis generates a conformational landscape; and (4) The ProDy ClustENM (D) protocol can be used for improving atomic structures.