https://3demmethods.i2pc.es/index.php?action=history&feed=atom&title=2023Vuillemot_MDTOMO 2026-05-01T09:52:07Z Revision history for this page on the wiki MediaWiki 1.44.2 https://3demmethods.i2pc.es/index.php?title=2023Vuillemot_MDTOMO&diff=4472&oldid=prev 2023-09-14T07:07:22Z

<p>Created page with &quot;== Citation == Vuillemot, Rémi / Rouiller, Isabelle / Jonić, Slavica. MDTOMO method for continuous conformational variability analysis in cryo electron subtomograms based o...&quot;</p> <p><b>New page</b></p><div>== Citation ==<br /> <br /> Vuillemot, Rémi / Rouiller, Isabelle / Jonić, Slavica. MDTOMO method for continuous conformational variability analysis in cryo electron subtomograms based on molecular dynamics simulations. 2023. Scientific Reports, Vol. 13, No. 1, p. 10596 <br /> <br /> == Abstract ==<br /> <br /> Cryo electron tomography (cryo-ET) allows observing macromolecular complexes in their native<br /> environment. The common routine of subtomogram averaging (STA) allows obtaining the threedimensional<br /> (3D) structure of abundant macromolecular complexes, and can be coupled with<br /> discrete classification to reveal conformational heterogeneity of the sample. However, the number<br /> of complexes extracted from cryo-ET data is usually small, which restricts the discrete-classification<br /> results to a small number of enough populated states and, thus, results in a largely incomplete<br /> conformational landscape. Alternative approaches are currently being investigated to explore the<br /> continuity of the conformational landscapes that in situ cryo-ET studies could provide. In this article,<br /> we present MDTOMO, a method for analyzing continuous conformational variability in cryo-ET<br /> subtomograms based on Molecular Dynamics (MD) simulations. MDTOMO allows obtaining an<br /> atomic-scale model of conformational variability and the corresponding free-energy landscape, from a<br /> given set of cryo-ET subtomograms. The article presents the performance of MDTOMO on a synthetic<br /> ABC exporter dataset and an in situ SARS-CoV-2 spike dataset. MDTOMO allows analyzing dynamic<br /> properties of molecular complexes to understand their biological functions, which could also be useful<br /> for structure-based drug discovery.<br /> <br /> == Keywords ==<br /> <br /> == Links ==<br /> <br /> https://www.nature.com/articles/s41598-023-37037-9<br /> <br /> == Related software ==<br /> <br /> == Related methods ==<br /> <br /> == Comments ==</div>

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