https://3demmethods.i2pc.es/index.php?action=history&feed=atom&title=2004Tama_NMA2 2026-05-24T19:52:18Z Revision history for this page on the wiki MediaWiki 1.44.2 https://3demmethods.i2pc.es/index.php?title=2004Tama_NMA2&diff=1562&oldid=prev 2009-04-02T16:16:43Z

<p></p> <p><b>New page</b></p><div>== Citation ==<br /> <br /> Tama F, Miyashita O, Brooks CL 3rd (2004b) Normal mode based<br /> flexible fitting of high-resolution structure into low-resolution<br /> experimental data from cryo-EM. J Struct Biol 147:315–326<br /> <br /> == Abstract ==<br /> <br /> A new method for the flexible fitting of high-resolution structures into low-resolution maps of macromolecular complexes from electron microscopy has been recently described in applications to simulated electron density maps. This method uses a linear combination of low-frequency normal modes in an iterative manner to deform the structure optimally to conform to the low-resolution electron density map. Gradient-following techniques in the coordinate space of collective normal modes are used to optimize the overall correlation coefficient between computed and measured electron densities. With this approach, multi-scale flexible fitting can be performed using all-atoms or Calpha atoms. In this paper, illustrative studies of normal mode based flexible fitting to experimental cryo-EM maps are presented for three different systems. Large, functionally relevant conformational changes for elongation factor G bound to the ribosome, Escherichia coli RNA polymerase and cowpea chlorotic mottle virus are elucidated as the result of the application of NMFF from high-resolution structures to cryo-electron microscopy maps.<br /> <br /> == Keywords ==<br /> <br /> NMA, normal modes, flexible fitting<br /> <br /> == Links ==<br /> <br /> Article http://www.ncbi.nlm.nih.gov/pubmed/15450300<br /> <br /> == Related software ==<br /> <br /> == Related methods ==<br /> <br /> == Comments ==</div>

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