https://3demmethods.i2pc.es/index.php?action=history&feed=atom&title=2008Orzechowski_Flexible 2026-05-24T20:41:44Z Revision history for this page on the wiki MediaWiki 1.44.2 https://3demmethods.i2pc.es/index.php?title=2008Orzechowski_Flexible&diff=4458&oldid=prev 2023-09-06T11:55:04Z

<p>Created page with &quot;== Citation == Orzechowski, Marek / Tama, Florence. Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics sim...&quot;</p> <p><b>New page</b></p><div>== Citation ==<br /> <br /> Orzechowski, Marek / Tama, Florence. Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations. 2008. <br /> Biophysical journal, Vol. 95, No. 12, p. 5692-5705 <br /> <br /> == Abstract ==<br /> <br /> A methodology for flexible fitting of all-atom high-resolution structures into low-resolution cryoelectron microscopy<br /> (cryo-EM) maps is presented. Flexibility of the modeled structure is simulated by classical molecular dynamics and an additional<br /> effective potential is introduced to enhance the fitting process. The additional potential is proportional to the correlation coefficient<br /> between the experimental cryo-EM map and a synthetic map generated for an all-atom structure being fitted to the map. The<br /> additional forces are calculated as a gradient of the correlation coefficient. During the molecular dynamics simulations under the<br /> additional forces, the molecule undergoes a conformational transition that maximizes the correlation coefficient, which results in a<br /> high-accuracy fit of all-atom structure into a cryo-EM map. Using five test proteins that exhibit structural rearrangement during their<br /> biological activity, we demonstrate performance of our method. We also test our method on the experimental cryo-EM of elongation<br /> factor G and show that the model obtained is comparable to previous studies. In addition, we show that overfitting can be avoided by<br /> assessing the quality of the fitted model in terms of correlation coefficient and secondary structure preservation.<br /> <br /> == Keywords ==<br /> <br /> == Links ==<br /> <br /> https://www.cell.com/biophysj/pdf/S0006-3495(08)81986-8.pdf<br /> <br /> == Related software ==<br /> <br /> == Related methods ==<br /> <br /> == Comments ==</div>

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