https://3demmethods.i2pc.es/index.php?action=history&feed=atom&title=2022Vuillemot_NMMD2022Vuillemot NMMD - Revision history2026-05-24T21:14:20ZRevision history for this page on the wikiMediaWiki 1.44.2https://3demmethods.i2pc.es/index.php?title=2022Vuillemot_NMMD&diff=4157&oldid=prevSjonic: Created page with "== Citation == Vuillemot, R.; Miyashita, O.; Tama, F.; Rouiller, I. & Jonic, S. NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynami..."2022-02-28T22:56:41Z<p>Created page with "== Citation == Vuillemot, R.; Miyashita, O.; Tama, F.; Rouiller, I. & Jonic, S. NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynami..."</p>
<p><b>New page</b></p><div>== Citation ==<br />
Vuillemot, R.; Miyashita, O.; Tama, F.; Rouiller, I. & Jonic, S. NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynamics atomic displacements. Journal of Molecular Biology, Volume 434, Issue 7, 2022, 167483.<br />
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== Abstract ==<br />
Atomic models of cryo electron microscopy (cryo-EM) maps of biomolecular conformations are often obtained by flexible fitting of the maps with available atomic structures of other conformations (e.g., obtained by X-ray crystallography). This article presents a new flexible fitting method, NMMD, which combines normal mode analysis (NMA) and molecular dynamics simulation (MD). Given an atomic structure and a cryo-EM map to fit, NMMD simultaneously estimates global atomic displacements based on NMA and local displacements based on MD. NMMD was implemented by modifying EMfit, a flexible fitting method using MD only, in GENESIS 1.4. As EMfit, NMMD can be run with replica exchange umbrella sampling procedure. The new method was tested using a variety of EM maps (synthetic and experimental, with different noise levels and resolutions). The results of the tests show that adding normal modes to MD-based fitting makes the fitting faster (40 % in average) and, in the majority of cases, more accurate. <br />
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== Keywords ==<br />
molecular modeling; cryo electron microscopy (cryo-EM); flexible fitting; normal mode analysis; molecular dynamics simulation<br />
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== Links ==<br />
https://doi.org/10.1016/j.jmb.2022.167483<br />
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== Related software ==<br />
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== Related methods ==<br />
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== Comments ==</div>Sjonic