https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_mode_analysis_(Phenylketonuria)&feed=atom&action=historyNormal mode analysis (Phenylketonuria) - Revision history2024-03-29T05:44:53ZRevision history for this page on the wikiMediaWiki 1.31.16https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_mode_analysis_(Phenylketonuria)&diff=38866&oldid=prevWorfk: /* Normal Mode Analysis */2013-09-05T21:20:09Z<p><span dir="auto"><span class="autocomment">Normal Mode Analysis</span></span></p>
<a href="https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_mode_analysis_(Phenylketonuria)&diff=38866&oldid=38865">Show changes</a>Worfkhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_mode_analysis_(Phenylketonuria)&diff=38865&oldid=prevWorfk: /* Summary */2013-09-05T21:01:10Z<p><span dir="auto"><span class="autocomment">Summary</span></span></p>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Summary ==</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>In this task we consider normal mode analysis (NMAs). A normal mode is described as a model of movement in an oscillating system. Thereby only [https://en.wikipedia.org/wiki/Harmonic_oscillator harmonic] motions can be captured by such analyses as the whole system must move with the same frequency, sinusoidally and with a fixed phase relation. Altogether, there are three types of motions with three atoms: the symmetric stretch, the antisymmetric stretch and the scissoring bend<del class="diffchange diffchange-inline"> </del><ref name="molWib"> [https://en.wikipedia.org/wiki/Molecular_vibration https://en.wikipedia.org/wiki/Molecular_vibration]: Molecular vibration, retrieved August 06, 2013. </ref>. To calculate such motions there is a three step algorithm. First a potential function for the system is generated. After that a matrix is calculated representing the force constants. In the last step this matrix is diagonalized. The eigenvectors then correspond to the normal modes and the eigenvalues to the frequency<del class="diffchange diffchange-inline">.</del><ref name="nm"> Dykeman et al. (2010): "[http://sankey.physics.asu.edu/Saguaro/notes/Eric_Dykeman_thesis.pdf Normal Mode Analysis and its applications in biological physics]" J. Phys.: Condens. Matter 22 [http://en.wikipedia.org/wiki/Digital_object_identifier doi]:[http://iopscience.iop.org/0953-8984/22/42/423202 10.1088/0953-8984/22/42/423202]</ref> As a matrix for all atoms would be problematic elastic models are created, where all atoms can be used. The atoms are connected with springs<ref name="elMod"> Altigan et al. (2001): "[http://www.sciencedirect.com/science/article/pii/S000634950176033X Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model]" Biophysical Journal 80, 505–515 [http://en.wikipedia.org/wiki/Digital_object_identifier doi]:[http://www.sciencedirect.com/science/article/pii/S000634950176033X 10.1016/S0006-3495(01)76033-X]</ref>.<br>In the following we used two different NMA tools. First we examine our protein PAH with [http://apps.cbu.uib.no/webnma/home WEBnm@] and then again with [http://www.igs.cnrs-mrs.fr/elnemo/start.html elNémo], which uses elastic networks. Provided animations are analysed showing the motions with lowest frequencies. Thereby we search for parts of the protein that move together and therefore indicating domains.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>In this task we consider normal mode analysis (NMAs). A normal mode is described as a model of movement in an oscillating system. Thereby only [https://en.wikipedia.org/wiki/Harmonic_oscillator harmonic] motions can be captured by such analyses as the whole system must move with the same frequency, sinusoidally and with a fixed phase relation. Altogether, there are three types of motions with three atoms: the symmetric stretch, the antisymmetric stretch and the scissoring bend<ref name="molWib"> [https://en.wikipedia.org/wiki/Molecular_vibration https://en.wikipedia.org/wiki/Molecular_vibration]: Molecular vibration, retrieved August 06, 2013. </ref>. To calculate such motions there is a three step algorithm. First a potential function for the system is generated. After that a matrix is calculated representing the force constants. In the last step this matrix is diagonalized. The eigenvectors then correspond to the normal modes and the eigenvalues to the frequency<ref name="nm"> Dykeman et al. (2010): "[http://sankey.physics.asu.edu/Saguaro/notes/Eric_Dykeman_thesis.pdf Normal Mode Analysis and its applications in biological physics]" J. Phys.: Condens. Matter 22 [http://en.wikipedia.org/wiki/Digital_object_identifier doi]:[http://iopscience.iop.org/0953-8984/22/42/423202 10.1088/0953-8984/22/42/423202]</ref><ins class="diffchange diffchange-inline">.</ins> As a matrix for all atoms would be problematic elastic models are created, where all atoms can be used. The atoms are connected with springs<ref name="elMod"> Altigan et al. (2001): "[http://www.sciencedirect.com/science/article/pii/S000634950176033X Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model]" Biophysical Journal 80, 505–515 [http://en.wikipedia.org/wiki/Digital_object_identifier doi]:[http://www.sciencedirect.com/science/article/pii/S000634950176033X 10.1016/S0006-3495(01)76033-X]</ref>.<br>In the following we used two different NMA tools. First we examine our protein PAH with [http://apps.cbu.uib.no/webnma/home WEBnm@] and then again with [http://www.igs.cnrs-mrs.fr/elnemo/start.html elNémo], which uses elastic networks. Provided animations are analysed showing the motions with lowest frequencies. Thereby we search for parts of the protein that move together and therefore indicating domains.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Normal Mode Analysis ==</div></td>
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</table>Worfkhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_mode_analysis_(Phenylketonuria)&diff=36455&oldid=prevWaldraffs at 08:58, 27 August 20132013-08-27T08:58:28Z<p></p>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Summary ==</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In this task we consider normal mode analysis (NMAs). A normal mode is described as a model of movement in an oscillating system. Thereby only [https://en.wikipedia.org/wiki/Harmonic_oscillator harmonic] motions can be captured by such analyses as the whole system must move with the same frequency, sinusoidally and with a fixed phase relation. Altogether, there are three types of motions with three atoms: the symmetric stretch, the antisymmetric stretch and the scissoring bend <ref name="molWib"> [https://en.wikipedia.org/wiki/Molecular_vibration https://en.wikipedia.org/wiki/Molecular_vibration]: Molecular vibration, retrieved August 06, 2013. </ref>. To calculate such motions there is a three step algorithm. First a potential function for the system is generated. After that a matrix is calculated representing the force constants. In the last step this matrix is diagonalized. The eigenvectors then correspond to the normal modes and the eigenvalues to the frequency.<ref name="nm"> Dykeman et al. (2010): "[http://sankey.physics.asu.edu/Saguaro/notes/Eric_Dykeman_thesis.pdf Normal Mode Analysis and its applications in biological physics]" J. Phys.: Condens. Matter 22 [http://en.wikipedia.org/wiki/Digital_object_identifier doi]:[http://iopscience.iop.org/0953-8984/22/42/423202 10.1088/0953-8984/22/42/423202]</ref> As a matrix for all atoms would be problematic elastic models are created, where all atoms can be used. The atoms are connected with springs<ref name="elMod"> Altigan et al. (2001): "[http://www.sciencedirect.com/science/article/pii/S000634950176033X Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model]" Biophysical Journal 80, 505–515 [http://en.wikipedia.org/wiki/Digital_object_identifier doi]:[http://www.sciencedirect.com/science/article/pii/S000634950176033X 10.1016/S0006-3495(01)76033-X]</ref>.<br>In the following we used two different NMA tools. First we examine our protein PAH with [http://apps.cbu.uib.no/webnma/home WEBnm@] and then again with [http://www.igs.cnrs-mrs.fr/elnemo/start.html elNémo], which uses elastic networks. Provided animations are analysed showing the motions with lowest frequencies. Thereby we search for parts of the protein that move together and therefore indicating domains.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In this task we consider normal mode analysis (NMAs). A normal mode is described as a model of movement in an oscillating system. Thereby only [https://en.wikipedia.org/wiki/Harmonic_oscillator harmonic] motions can be captured by such analyses as the whole system must move with the same frequency, sinusoidally and with a fixed phase relation. Altogether, there are three types of motions with three atoms: the symmetric stretch, the antisymmetric stretch and the scissoring bend <ref name="molWib"> [https://en.wikipedia.org/wiki/Molecular_vibration https://en.wikipedia.org/wiki/Molecular_vibration]: Molecular vibration, retrieved August 06, 2013. </ref>. To calculate such motions there is a three step algorithm. First a potential function for the system is generated. After that a matrix is calculated representing the force constants. In the last step this matrix is diagonalized. The eigenvectors then correspond to the normal modes and the eigenvalues to the frequency.<ref name="nm"> Dykeman et al. (2010): "[http://sankey.physics.asu.edu/Saguaro/notes/Eric_Dykeman_thesis.pdf Normal Mode Analysis and its applications in biological physics]" J. Phys.: Condens. Matter 22 [http://en.wikipedia.org/wiki/Digital_object_identifier doi]:[http://iopscience.iop.org/0953-8984/22/42/423202 10.1088/0953-8984/22/42/423202]</ref> As a matrix for all atoms would be problematic elastic models are created, where all atoms can be used. The atoms are connected with springs<ref name="elMod"> Altigan et al. (2001): "[http://www.sciencedirect.com/science/article/pii/S000634950176033X Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model]" Biophysical Journal 80, 505–515 [http://en.wikipedia.org/wiki/Digital_object_identifier doi]:[http://www.sciencedirect.com/science/article/pii/S000634950176033X 10.1016/S0006-3495(01)76033-X]</ref>.<br>In the following we used two different NMA tools. First we examine our protein PAH with [http://apps.cbu.uib.no/webnma/home WEBnm@] and then again with [http://www.igs.cnrs-mrs.fr/elnemo/start.html elNémo], which uses elastic networks. Provided animations are analysed showing the motions with lowest frequencies. Thereby we search for parts of the protein that move together and therefore indicating domains.</div></td>
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</table>Waldraffshttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_mode_analysis_(Phenylketonuria)&diff=35241&oldid=prevWaldraffs: /* Mode11 */2013-08-17T14:43:01Z<p><span dir="auto"><span class="autocomment">Mode11</span></span></p>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="mode11_matrix"><small>[[File:PAH_mode11_matrix.png|thumb|right|300px|'''<caption>'''Matrix showing the maximal distance fluctuation of PAH (pdb 1J8U). If the distances decrease they are plotted in red, whereas increasing distances are shown in blue, but only if they are under the 10% strongest distance changes.</caption>]]</small></figure></div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The fluctuation of mode 11 of PAH (<xr id="mode11_gif"/>) looks very similar to mode 9 (<xr id="mode9_gif"/>) with a "breathing" movement. Additionally the matrices have some resemblances. However, in this case (xr id="mode11_matrix"/>) there are more increasing distances and only at residue 180 the decreasing distance to the last 20 residues can be seen. This one seems to have no corresponding mode in WEBnm@.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The fluctuation of mode 11 of PAH (<xr id="mode11_gif"/>) looks very similar to mode 9 (<xr id="mode9_gif"/>) with a "breathing" movement. Additionally the matrices have some resemblances. However, in this case (<ins class="diffchange diffchange-inline"><</ins>xr id="mode11_matrix"/>) there are more increasing distances and only at residue 180 the decreasing distance to the last 20 residues can be seen. This one seems to have no corresponding mode in WEBnm@.</div></td>
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</table>Waldraffshttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_mode_analysis_(Phenylketonuria)&diff=35240&oldid=prevWaldraffs: /* Mode10 */2013-08-17T14:42:45Z<p><span dir="auto"><span class="autocomment">Mode10</span></span></p>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[File:PAH_mode10_3.gif|thumb|left|300px|'''<caption>''' Representation of the PAH (pdb 1J8U) movement calculated by elNémo. </caption>]]</small></figure></div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[File:PAH_mode10_3.gif|thumb|left|300px|'''<caption>''' Representation of the PAH (pdb 1J8U) movement calculated by elNémo. </caption>]]</small></figure></div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="mode10_matrix"><small>[[File:PAH_mode10_matrix.png|thumb|right|300px|'''<caption>'''Matrix showing the maximal distance fluctuation of PAH (pdb 1J8U). If the distances decrease they are plotted in red, whereas increasing distances are shown in blue, but only if they are under the 10% strongest distance changes.</caption>]]</small></figure></div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="mode10_matrix"><small>[[File:PAH_mode10_matrix.png|thumb|right|300px|'''<caption>'''Matrix showing the maximal distance fluctuation of PAH (pdb 1J8U). If the distances decrease they are plotted in red, whereas increasing distances are shown in blue, but only if they are under the 10% strongest distance changes.</caption>]]</small></figure></div></td>
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<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Mode 10 (<xr id="mode10_gif"/>) has some similarities with mode 8 showing a hinge-movement. Also the &beta;-strand on the right shows no fluctuation. <xr id="mode10_matrix"/> shows some movements on different parts of the protein. In comparison with the modes found with WEBnm@ this mode has some resemblances with both mode 10 and 11. </div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Mode 10 (<xr id="mode10_gif"/>) has some similarities with mode 8 showing a hinge-movement. Also the &beta;-strand on the right shows<ins class="diffchange diffchange-inline"> nearly</ins> no fluctuation. <xr id="mode10_matrix"/> shows some movements on different parts of the protein. In comparison with the modes found with WEBnm@ this mode has some resemblances with both mode 10 and 11. </div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br clear=all></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br clear=all></div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
</table>Waldraffshttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_mode_analysis_(Phenylketonuria)&diff=35239&oldid=prevWaldraffs: /* Mode8 */2013-08-17T14:42:14Z<p><span dir="auto"><span class="autocomment">Mode8</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 14:42, 17 August 2013</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 105:</td>
<td colspan="2" class="diff-lineno">Line 105:</td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[File:PAH_mode8_3.gif|thumb|left|300px|'''<caption>''' Representation of the PAH (pdb 1J8U) movement calculated by elNémo. </caption>]]</small></figure></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[File:PAH_mode8_3.gif|thumb|left|300px|'''<caption>''' Representation of the PAH (pdb 1J8U) movement calculated by elNémo. </caption>]]</small></figure></div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="mode8_matrix"><small>[[File:PAH_mode8_matrix.png|thumb|right|300px|'''<caption>'''Matrix showing the maximal distance fluctuation of PAH (pdb 1J8U). If the distances decrease they are plotted in red, whereas increasing distances are shown in blue, but only if they are under the 10% strongest distance changes.</caption>]]</small></figure></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="mode8_matrix"><small>[[File:PAH_mode8_matrix.png|thumb|right|300px|'''<caption>'''Matrix showing the maximal distance fluctuation of PAH (pdb 1J8U). If the distances decrease they are plotted in red, whereas increasing distances are shown in blue, but only if they are under the 10% strongest distance changes.</caption>]]</small></figure></div></td>
</tr>
<tr>
<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>In <xr id="mode8_gif"/> you can see that the protein opens and closes at the binding site, whereby it looks like an opening and closing mouth. So this mode shows a hinge-movement for our protein PAH. The &beta;-strand (red) does not move. Additionally in the correlation matrix (<xr id="mode8_matrix"/>) only small parts of the protein seem to move at all and the distances hardly ever increase, but decrease. In WEBnm@ a similar movement can be seen in mode 8 with just a few residues moving.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>In <xr id="mode8_gif"/> you can see that the protein opens and closes at the binding site, whereby it looks like an opening and closing mouth. So this mode shows a hinge-movement for our protein PAH. The &beta;-strand (red) does not move<ins class="diffchange diffchange-inline"> much</ins>. Additionally in the correlation matrix (<xr id="mode8_matrix"/>) only small parts of the protein seem to move at all and the distances hardly ever increase, but decrease. In WEBnm@ a similar movement can be seen in mode 8 with just a few residues moving.</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br clear=all></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br clear=all></div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
</table>Waldraffshttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_mode_analysis_(Phenylketonuria)&diff=35238&oldid=prevWaldraffs: /* WEBnm@ */2013-08-17T14:39:43Z<p><span dir="auto"><span class="autocomment">WEBnm@</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 14:39, 17 August 2013</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 13:</td>
<td colspan="2" class="diff-lineno">Line 13:</td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==== Mode 7 ====</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==== Mode 7 ====</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_mode7"><small>[[File:PAH_1j8u_mode7.png|thumb|left|300px|'''<caption>'''Mode 7 captured of WEBnm@. The PAH structure (pdb 1j8u) is shown in transperent green, the ligands in red (H4B: C<sub>9</sub>H<sub>15</sub>N<sub>5</sub>O<sub>3</sub>) and orange (Fe<sub>2</sub>). The blue doted lines represent the movement of the structure. </caption>]]</small></figure></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_mode7"><small>[[File:PAH_1j8u_mode7.png|thumb|left|300px|'''<caption>'''Mode 7 captured of WEBnm@. The PAH structure (pdb 1j8u) is shown in transperent green, the ligands in red (H4B: C<sub>9</sub>H<sub>15</sub>N<sub>5</sub>O<sub>3</sub>) and orange (Fe<sub>2</sub>). The blue doted lines represent the movement of the structure. </caption>]]</small></figure></div></td>
</tr>
<tr>
<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_plot7"><small>[[File:pah_1j8u.pdb.mode7plot.png|thumb|right|300px|'''<caption><del class="diffchange diffchange-inline">'</del>'''Normalized squared displacement per residue for mode 7 to 12. The x-axis represent the residue number in the sequence, whereby 0 is the first of the structure sequence, which is residue 103 in the FASTA-sequence of P00439. the y-axis shows the normalized squared displacement.</caption>]]</small></figure></div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_plot7"><small>[[File:pah_1j8u.pdb.mode7plot.png|thumb|right|300px|'''<caption>'''Normalized squared displacement per residue for mode 7 to 12. The x-axis represent the residue number in the sequence, whereby 0 is the first of the structure sequence, which is residue 103 in the FASTA-sequence of P00439. the y-axis shows the normalized squared displacement.</caption>]]</small></figure></div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>This mode seems to have a high movement as the blue dotted lines in <xr id="web_mode7"/> are relatively long. Furthermore they seem to open and close on all sites the same, which gives the imagine of a pump and not a twist. We additionally looked at the movement provided by the webserver, where the "breathing" rhythm could be seen, too. This also can be viewed in <xr id="web_plot7"/>. Between residues 20 and 30 there is a high atomic displacement which also can be seen for residues 240 to 300. </div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>This mode seems to have a high movement as the blue dotted lines in <xr id="web_mode7"/> are relatively long. Furthermore they seem to open and close on all sites the same, which gives the imagine of a pump and not a twist. We additionally looked at the movement provided by the webserver, where the "breathing" rhythm could be seen, too. This also can be viewed in <xr id="web_plot7"/>. Between residues 20 and 30 there is a high atomic displacement which also can be seen for residues 240 to 300. </div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td colspan="2" class="diff-lineno">Line 20:</td>
<td colspan="2" class="diff-lineno">Line 20:</td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==== Mode 8 ====</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==== Mode 8 ====</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_mode8"><small>[[File:PAH_1j8u_mode8.png|thumb|left|300px|'''<caption>'''Mode 8 captured of WEBnm@. The PAH structure (pdb 1j8u) is shown in transperent green, the ligands in red (H4B: C<sub>9</sub>H<sub>15</sub>N<sub>5</sub>O<sub>3</sub>) and orange (Fe<sub>2</sub>). The blue doted lines represent the movement of the structure. </caption>]]</small></figure></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_mode8"><small>[[File:PAH_1j8u_mode8.png|thumb|left|300px|'''<caption>'''Mode 8 captured of WEBnm@. The PAH structure (pdb 1j8u) is shown in transperent green, the ligands in red (H4B: C<sub>9</sub>H<sub>15</sub>N<sub>5</sub>O<sub>3</sub>) and orange (Fe<sub>2</sub>). The blue doted lines represent the movement of the structure. </caption>]]</small></figure></div></td>
</tr>
<tr>
<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_plot8"><small>[[File:pah_1j8u.pdb.mode8plot.png|thumb|right|300px|'''<caption><del class="diffchange diffchange-inline">'</del>'''Normalized squared displacement per residue for mode 7 to 12. The x-axis represent the residue number in the sequence, whereby 0 is the first of the structure sequence, which is residue 103 in the FASTA-sequence of P00439. the y-axis shows the normalized squared displacement.</caption>]]</small></figure></div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_plot8"><small>[[File:pah_1j8u.pdb.mode8plot.png|thumb|right|300px|'''<caption>'''Normalized squared displacement per residue for mode 7 to 12. The x-axis represent the residue number in the sequence, whereby 0 is the first of the structure sequence, which is residue 103 in the FASTA-sequence of P00439. the y-axis shows the normalized squared displacement.</caption>]]</small></figure></div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Mode 8 of WEBnm@ show a few differences to mode 7 as there seems only be a atomic displacement at residues 20 to 50 (<xr id="web_plot8"/>). In <xr id="web_mode8"/> you can see that this is represented in the picture on the right site of the binding site. The animation looks like a hinge-movement. Maybe this helps the protein to bind or release a substrate.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Mode 8 of WEBnm@ show a few differences to mode 7 as there seems only be a atomic displacement at residues 20 to 50 (<xr id="web_plot8"/>). In <xr id="web_mode8"/> you can see that this is represented in the picture on the right site of the binding site. The animation looks like a hinge-movement. Maybe this helps the protein to bind or release a substrate.</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td colspan="2" class="diff-lineno">Line 27:</td>
<td colspan="2" class="diff-lineno">Line 27:</td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==== Mode 9 ====</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==== Mode 9 ====</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_mode9"><small>[[File:PAH_1j8u_mode9.png|thumb|left|300px|'''<caption>'''Mode 9 captured of WEBnm@.The PAH structure (pdb 1j8u) is shown in transperent green, the ligands in red (H4B: C<sub>9</sub>H<sub>15</sub>N<sub>5</sub>O<sub>3</sub>) and orange (Fe<sub>2</sub>). The blue doted lines represent the movement of the structure.</caption>]]</small></figure></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_mode9"><small>[[File:PAH_1j8u_mode9.png|thumb|left|300px|'''<caption>'''Mode 9 captured of WEBnm@.The PAH structure (pdb 1j8u) is shown in transperent green, the ligands in red (H4B: C<sub>9</sub>H<sub>15</sub>N<sub>5</sub>O<sub>3</sub>) and orange (Fe<sub>2</sub>). The blue doted lines represent the movement of the structure.</caption>]]</small></figure></div></td>
</tr>
<tr>
<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_plot9"><small>[[File:pah_1j8u.pdb.mode9plot.png|thumb|right|300px|'''<caption><del class="diffchange diffchange-inline">'</del>'''Normalized squared displacement per residue for mode 7 to 12. The x-axis represent the residue number in the sequence, whereby 0 is the first of the structure sequence, which is residue 103 in the FASTA-sequence of P00439. the y-axis shows the normalized squared displacement.</caption>]]</small></figure></div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_plot9"><small>[[File:pah_1j8u.pdb.mode9plot.png|thumb|right|300px|'''<caption>'''Normalized squared displacement per residue for mode 7 to 12. The x-axis represent the residue number in the sequence, whereby 0 is the first of the structure sequence, which is residue 103 in the FASTA-sequence of P00439. the y-axis shows the normalized squared displacement.</caption>]]</small></figure></div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Like in the mode before there is only a part of the protein showing a high atomic displacement. This part is between the residues 280 and 310 (<xr id="web_plot9"/>). However, there is also a small part in the beginning which shows atomic displacement of about 2 in the normalized value.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Like in the mode before there is only a part of the protein showing a high atomic displacement. This part is between the residues 280 and 310 (<xr id="web_plot9"/>). However, there is also a small part in the beginning which shows atomic displacement of about 2 in the normalized value.</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Also you can see in <xr id="web_mode9"/> that there are two parts of the protein that have a high fluctuation, which is at the top of the picture and at the right. The vectors on the right seem to show a backward movement. With all parts moving on the same time, the binding site seems to be opened and closed by this movement.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Also you can see in <xr id="web_mode9"/> that there are two parts of the protein that have a high fluctuation, which is at the top of the picture and at the right. The vectors on the right seem to show a backward movement. With all parts moving on the same time, the binding site seems to be opened and closed by this movement.</div></td>
</tr>
<tr>
<td colspan="2" class="diff-lineno">Line 35:</td>
<td colspan="2" class="diff-lineno">Line 35:</td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==== Mode 10 ====</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==== Mode 10 ====</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_mode10"><small>[[File:PAH_1j8u_mode10.png|thumb|left|300px|'''<caption>'''Mode 10 captured of WEBnm@. The PAH structure (pdb 1j8u) is shown in transperent green, the ligands in red (H4B: C<sub>9</sub>H<sub>15</sub>N<sub>5</sub>O<sub>3</sub>) and orange (Fe<sub>2</sub>). The blue doted lines represent the movement of the structure.</caption>]]</small></figure></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_mode10"><small>[[File:PAH_1j8u_mode10.png|thumb|left|300px|'''<caption>'''Mode 10 captured of WEBnm@. The PAH structure (pdb 1j8u) is shown in transperent green, the ligands in red (H4B: C<sub>9</sub>H<sub>15</sub>N<sub>5</sub>O<sub>3</sub>) and orange (Fe<sub>2</sub>). The blue doted lines represent the movement of the structure.</caption>]]</small></figure></div></td>
</tr>
<tr>
<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_plot10"><small>[[File:pah_1j8u.pdb.mode10plot.png|thumb|right|300px|'''<caption><del class="diffchange diffchange-inline">'</del>'''Normalized squared displacement per residue for mode 7 to 12. The x-axis represent the residue number in the sequence, whereby 0 is the first of the structure sequence, which is residue 103 in the FASTA-sequence of P00439. the y-axis shows the normalized squared displacement.</caption>]]</small></figure></div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_plot10"><small>[[File:pah_1j8u.pdb.mode10plot.png|thumb|right|300px|'''<caption>'''Normalized squared displacement per residue for mode 7 to 12. The x-axis represent the residue number in the sequence, whereby 0 is the first of the structure sequence, which is residue 103 in the FASTA-sequence of P00439. the y-axis shows the normalized squared displacement.</caption>]]</small></figure></div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Mode 10 shows a high atomic displacement in some parts of the protein. Especially in the beginning before residue 50 and again after residue 280 (<xr id="web_plot10"/>). However, in <xr id="web_mode10"/> there seems to be not that much movement. In this case the fluctuation seems to go in the direction of the binding site and thereby constricting this.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Mode 10 shows a high atomic displacement in some parts of the protein. Especially in the beginning before residue 50 and again after residue 280 (<xr id="web_plot10"/>). However, in <xr id="web_mode10"/> there seems to be not that much movement. In this case the fluctuation seems to go in the direction of the binding site and thereby constricting this.</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td colspan="2" class="diff-lineno">Line 42:</td>
<td colspan="2" class="diff-lineno">Line 42:</td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==== Mode 11 ====</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==== Mode 11 ====</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_mode11"><small>[[File:PAH_1j8u_mode11.png|thumb|left|300px|'''<caption>'''Mode 11 captured of WEBnm@. The PAH structure (pdb 1j8u) is shown in transperent green, the ligands in red (H4B: C<sub>9</sub>H<sub>15</sub>N<sub>5</sub>O<sub>3</sub>) and orange (Fe<sub>2</sub>). The blue doted lines represent the movement of the structure.</caption>]]</small></figure></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_mode11"><small>[[File:PAH_1j8u_mode11.png|thumb|left|300px|'''<caption>'''Mode 11 captured of WEBnm@. The PAH structure (pdb 1j8u) is shown in transperent green, the ligands in red (H4B: C<sub>9</sub>H<sub>15</sub>N<sub>5</sub>O<sub>3</sub>) and orange (Fe<sub>2</sub>). The blue doted lines represent the movement of the structure.</caption>]]</small></figure></div></td>
</tr>
<tr>
<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_plot11"><small>[[File:pah_1j8u.pdb.mode11plot.png|thumb|right|300px|'''<caption><del class="diffchange diffchange-inline">'</del>'''Normalized squared displacement per residue for mode 7 to 12. The x-axis represent the residue number in the sequence, whereby 0 is the first of the structure sequence, which is residue 103 in the FASTA-sequence of P00439. the y-axis shows the normalized squared displacement.</caption>]]</small></figure></div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_plot11"><small>[[File:pah_1j8u.pdb.mode11plot.png|thumb|right|300px|'''<caption>'''Normalized squared displacement per residue for mode 7 to 12. The x-axis represent the residue number in the sequence, whereby 0 is the first of the structure sequence, which is residue 103 in the FASTA-sequence of P00439. the y-axis shows the normalized squared displacement.</caption>]]</small></figure></div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>This mode seems to have some similarities with mode 10 in the atomic displacement as there is a high atomic displacement in the beginning and in the end of the protein (<xr id="web_plot11"/>). However, looking at <xr id="web_mode11"/> some differences can be viewed like in the bottom left of the picture, where you can see that the movement has another direction and may be indicate a small twist instead of the closing fluctuation. </div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>This mode seems to have some similarities with mode 10 in the atomic displacement as there is a high atomic displacement in the beginning and in the end of the protein (<xr id="web_plot11"/>). However, looking at <xr id="web_mode11"/> some differences can be viewed like in the bottom left of the picture, where you can see that the movement has another direction and may be indicate a small twist instead of the closing fluctuation. </div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td colspan="2" class="diff-lineno">Line 49:</td>
<td colspan="2" class="diff-lineno">Line 49:</td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==== Mode 12 ====</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==== Mode 12 ====</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_mode12"><small>[[File:PAH_1j8u_mode12.png|thumb|left|300px|'''<caption>'''Mode 12 captured of WEBnm@. The PAH structure (pdb 1j8u) is shown in transperent green, the ligands in red (H4B: C<sub>9</sub>H<sub>15</sub>N<sub>5</sub>O<sub>3</sub>) and orange (Fe<sub>2</sub>). The blue doted lines represent the movement of the structure.</caption>]]</small></figure></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_mode12"><small>[[File:PAH_1j8u_mode12.png|thumb|left|300px|'''<caption>'''Mode 12 captured of WEBnm@. The PAH structure (pdb 1j8u) is shown in transperent green, the ligands in red (H4B: C<sub>9</sub>H<sub>15</sub>N<sub>5</sub>O<sub>3</sub>) and orange (Fe<sub>2</sub>). The blue doted lines represent the movement of the structure.</caption>]]</small></figure></div></td>
</tr>
<tr>
<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_plot12"><small>[[File:pah_1j8u.pdb.mode12plot.png|thumb|right|300px|'''<caption><del class="diffchange diffchange-inline">'</del>'''Normalized squared displacement per residue for mode 7 to 12. The x-axis represent the residue number in the sequence, whereby 0 is the first of the structure sequence, which is residue 103 in the FASTA-sequence of P00439. the y-axis shows the normalized squared displacement.</caption>]]</small></figure></div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_plot12"><small>[[File:pah_1j8u.pdb.mode12plot.png|thumb|right|300px|'''<caption>'''Normalized squared displacement per residue for mode 7 to 12. The x-axis represent the residue number in the sequence, whereby 0 is the first of the structure sequence, which is residue 103 in the FASTA-sequence of P00439. the y-axis shows the normalized squared displacement.</caption>]]</small></figure></div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The last mode in this task provided by WEBnm@ shows highest atomic displacement at residues 25 to 50 (<xr id="web_plot12"/>), but also in the rest of the protein, which also can be vied in <xr id="web_mode12"/>. Nevertheless in the upper part of the picture only small vectors are shown, which indicates only small motion, whereas on the lower part there seemes to be a left to right movement in the foreground of the protein in this snapshot.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The last mode in this task provided by WEBnm@ shows highest atomic displacement at residues 25 to 50 (<xr id="web_plot12"/>), but also in the rest of the protein, which also can be vied in <xr id="web_mode12"/>. Nevertheless in the upper part of the picture only small vectors are shown, which indicates only small motion, whereas on the lower part there seemes to be a left to right movement in the foreground of the protein in this snapshot.</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br clear=all></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br clear=all></div></td>
</tr>
</table>Waldraffshttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_mode_analysis_(Phenylketonuria)&diff=35160&oldid=prevWaldraffs: /* Mode 7 */2013-08-17T08:55:06Z<p><span dir="auto"><span class="autocomment">Mode 7</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 08:55, 17 August 2013</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 14:</td>
<td colspan="2" class="diff-lineno">Line 14:</td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_mode7"><small>[[File:PAH_1j8u_mode7.png|thumb|left|300px|'''<caption>'''Mode 7 captured of WEBnm@. The PAH structure (pdb 1j8u) is shown in transperent green, the ligands in red (H4B: C<sub>9</sub>H<sub>15</sub>N<sub>5</sub>O<sub>3</sub>) and orange (Fe<sub>2</sub>). The blue doted lines represent the movement of the structure. </caption>]]</small></figure></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_mode7"><small>[[File:PAH_1j8u_mode7.png|thumb|left|300px|'''<caption>'''Mode 7 captured of WEBnm@. The PAH structure (pdb 1j8u) is shown in transperent green, the ligands in red (H4B: C<sub>9</sub>H<sub>15</sub>N<sub>5</sub>O<sub>3</sub>) and orange (Fe<sub>2</sub>). The blue doted lines represent the movement of the structure. </caption>]]</small></figure></div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_plot7"><small>[[File:pah_1j8u.pdb.mode7plot.png|thumb|right|300px|'''<caption>''''Normalized squared displacement per residue for mode 7 to 12. The x-axis represent the residue number in the sequence, whereby 0 is the first of the structure sequence, which is residue 103 in the FASTA-sequence of P00439. the y-axis shows the normalized squared displacement.</caption>]]</small></figure></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="web_plot7"><small>[[File:pah_1j8u.pdb.mode7plot.png|thumb|right|300px|'''<caption>''''Normalized squared displacement per residue for mode 7 to 12. The x-axis represent the residue number in the sequence, whereby 0 is the first of the structure sequence, which is residue 103 in the FASTA-sequence of P00439. the y-axis shows the normalized squared displacement.</caption>]]</small></figure></div></td>
</tr>
<tr>
<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>This mode seems to have a high movement as the blue <del class="diffchange diffchange-inline">doted</del> lines in <xr id="web_mode7"/> are relatively long. Furthermore they seem to open and close on all sites the same, which gives the imagine of a pump and not a twist. We additionally looked at the movement provided by the webserver, where the "breathing" rhythm could be seen, too. This also can be viewed in <xr id="web_plot7"/>. Between residues 20 and 30 there is a high atomic displacement which also can be seen for residues 240 to 300. </div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>This mode seems to have a high movement as the blue <ins class="diffchange diffchange-inline">dotted</ins> lines in <xr id="web_mode7"/> are relatively long. Furthermore they seem to open and close on all sites the same, which gives the imagine of a pump and not a twist. We additionally looked at the movement provided by the webserver, where the "breathing" rhythm could be seen, too. This also can be viewed in <xr id="web_plot7"/>. Between residues 20 and 30 there is a high atomic displacement which also can be seen for residues 240 to 300. </div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br clear=all></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br clear=all></div></td>
</tr>
</table>Waldraffshttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_mode_analysis_(Phenylketonuria)&diff=34975&oldid=prevWorfk: /* Summary */2013-08-13T12:59:52Z<p><span dir="auto"><span class="autocomment">Summary</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 12:59, 13 August 2013</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td>
</tr>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Summary ==</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Summary ==</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>In this task we consider normal mode analysis (NMAs). A normal mode is described as a model of movement in an oscillating system. Thereby only [https://en.wikipedia.org/wiki/Harmonic_oscillator harmonic] motions can be captured by such analyses as the whole system must move with the same frequency, sinusoidally and with a fixed phase relation. Altogether, there are three types of motions with three atoms: the symmetric stretch, the antisymmetric stretch and the scissoring bend <ref name="molWib"> [https://en.wikipedia.org/wiki/Molecular_vibration https://en.wikipedia.org/wiki/Molecular_vibration]: Molecular vibration, retrieved August 06, 2013. </ref> To calculate such motions there is a three step algorithm. First a potential function for the system is generated. After that a matrix is calculated representing the force constants. In the last step this matrix is diagonalized. The eigenvectors then correspond to the normal modes and the eigenvalues to the frequency.<ref name="nm"> Dykeman et al. (2010): "[http://sankey.physics.asu.edu/Saguaro/notes/Eric_Dykeman_thesis.pdf Normal Mode Analysis and its applications in biological physics]" J. Phys.: Condens. Matter 22 [http://en.wikipedia.org/wiki/Digital_object_identifier doi]:[http://iopscience.iop.org/0953-8984/22/42/423202 10.1088/0953-8984/22/42/423202]</ref> As a matrix for all atoms would be problematic elastic models are created, where all atoms can be used. The atoms are connected with springs<ref name="elMod"> Altigan et al. (2001): "[http://www.sciencedirect.com/science/article/pii/S000634950176033X Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model]" Biophysical Journal 80, 505–515 [http://en.wikipedia.org/wiki/Digital_object_identifier doi]:[http://www.sciencedirect.com/science/article/pii/S000634950176033X 10.1016/S0006-3495(01)76033-X]</ref>.<br>In the following we used two different NMA tools. First we examine our protein PAH with [http://apps.cbu.uib.no/webnma/home WEBnm@] and then again with [http://www.igs.cnrs-mrs.fr/elnemo/start.html elNémo], which uses elastic networks. Provided animations are analysed showing the motions with lowest frequencies. Thereby we search for parts of the protein that move together and therefore indicating domains.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>In this task we consider normal mode analysis (NMAs). A normal mode is described as a model of movement in an oscillating system. Thereby only [https://en.wikipedia.org/wiki/Harmonic_oscillator harmonic] motions can be captured by such analyses as the whole system must move with the same frequency, sinusoidally and with a fixed phase relation. Altogether, there are three types of motions with three atoms: the symmetric stretch, the antisymmetric stretch and the scissoring bend <ref name="molWib"> [https://en.wikipedia.org/wiki/Molecular_vibration https://en.wikipedia.org/wiki/Molecular_vibration]: Molecular vibration, retrieved August 06, 2013. </ref><ins class="diffchange diffchange-inline">.</ins> To calculate such motions there is a three step algorithm. First a potential function for the system is generated. After that a matrix is calculated representing the force constants. In the last step this matrix is diagonalized. The eigenvectors then correspond to the normal modes and the eigenvalues to the frequency.<ref name="nm"> Dykeman et al. (2010): "[http://sankey.physics.asu.edu/Saguaro/notes/Eric_Dykeman_thesis.pdf Normal Mode Analysis and its applications in biological physics]" J. Phys.: Condens. Matter 22 [http://en.wikipedia.org/wiki/Digital_object_identifier doi]:[http://iopscience.iop.org/0953-8984/22/42/423202 10.1088/0953-8984/22/42/423202]</ref> As a matrix for all atoms would be problematic elastic models are created, where all atoms can be used. The atoms are connected with springs<ref name="elMod"> Altigan et al. (2001): "[http://www.sciencedirect.com/science/article/pii/S000634950176033X Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model]" Biophysical Journal 80, 505–515 [http://en.wikipedia.org/wiki/Digital_object_identifier doi]:[http://www.sciencedirect.com/science/article/pii/S000634950176033X 10.1016/S0006-3495(01)76033-X]</ref>.<br>In the following we used two different NMA tools. First we examine our protein PAH with [http://apps.cbu.uib.no/webnma/home WEBnm@] and then again with [http://www.igs.cnrs-mrs.fr/elnemo/start.html elNémo], which uses elastic networks. Provided animations are analysed showing the motions with lowest frequencies. Thereby we search for parts of the protein that move together and therefore indicating domains.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Normal Mode Analysis ==</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Normal Mode Analysis ==</div></td>
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</table>Worfkhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_mode_analysis_(Phenylketonuria)&diff=34034&oldid=prevWaldraffs: /* elNémo */2013-08-06T09:08:57Z<p><span dir="auto"><span class="autocomment">elNémo</span></span></p>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><small><center>'''<caption>'''The five modes with lowest frequency for the protein PAH (pdb 1J8U). The first column represents the mode the second one the frequency and the third the collectivity<ins class="diffchange diffchange-inline">. Mode 10 has a particullary low collectivity (marked in green)</ins>.</caption></center></small></div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*B-factor analysis for the correlation between observed and normal-mode-derived atomi displacement parameters: </div></td>
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