https://3demmethods.i2pc.es/index.php?action=history&feed=atom&title=2024Yoshidome_4D 2026-06-13T12:18:02Z Revision history for this page on the wiki MediaWiki 1.44.2 https://3demmethods.i2pc.es/index.php?title=2024Yoshidome_4D&diff=4578&oldid=prev 2024-07-31T05:54:23Z

<p>Created page with &quot;== Citation == Yoshidome, Takashi. Four-dimensional imaging for cryo-electron microscopy experiments using molecular simulations and manifold learning. 2024. J. Computational Chemistry, Vol. 45, No. 11, p. 738-751 == Abstract == Elucidating protein conformational changes is essential because conformational changes are closely related to the functions of proteins. Cryo-electron microscopy (cryo-EM) experiment can be used to reconstruct protein conformational changes vi...&quot;</p> <p><b>New page</b></p><div>== Citation ==<br /> <br /> Yoshidome, Takashi. Four-dimensional imaging for cryo-electron microscopy experiments using molecular simulations and manifold learning. 2024. J. Computational Chemistry, Vol. 45, No. 11, p. 738-751<br /> <br /> == Abstract ==<br /> <br /> Elucidating protein conformational changes is essential because conformational<br /> changes are closely related to the functions of proteins. Cryo-electron microscopy<br /> (cryo-EM) experiment can be used to reconstruct protein conformational changes via<br /> a method that involves using the experimental data (two-dimensional protein<br /> images). In this study, a reconstruction method, referred to as the “four-dimensional<br /> imaging,” was proposed. In our four-dimensional imaging technique, the protein conformational<br /> change was obtained using the two-dimensional protein images (the<br /> three-dimensional electron density maps used in previously proposed techniques<br /> were not used). The protein conformation for each two-dimensional protein image<br /> was obtained using our original protocol with molecular dynamics simulations. Using<br /> a manifold-learning technique and two-dimensional protein images, the protein conformations<br /> were arranged according to the conformational change of the protein. By<br /> arranging the protein conformations according to the arrangement of the protein<br /> images, four-dimensional imaging is constructed. A simulation for a cryo-EM experiment<br /> demonstrated the validity of our four-dimensional imaging technique.<br /> <br /> == Keywords ==<br /> <br /> == Links ==<br /> <br /> https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.27290<br /> <br /> == Related software ==<br /> <br /> == Related methods ==<br /> <br /> == Comments ==</div>

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