https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_BCKDHA&feed=atom&action=historyNormal Mode Analysis BCKDHA - Revision history2024-03-28T08:11:11ZRevision history for this page on the wikiMediaWiki 1.31.16https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_BCKDHA&diff=15790&oldid=prevDemel: /* Comparison of the lowest-frequency normal modes with the MD simulation */2011-09-29T08:40:29Z<p><span dir="auto"><span class="autocomment">Comparison of the lowest-frequency normal modes with the MD simulation</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<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 08:40, 29 September 2011</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>By comparing the normal modes (Figure 56a-e)with the MD simulation (Figure 57) we can see that the model of MD is much more detailed than the normal modes as it is possible to see the motion of the side chains and not only of the domains or secondary structures. Additionally the protein which is simulated by MD shows much more motion in the whole cell and does not seem to be sticked at one position.<br></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>By comparing the normal modes (Figure 56a-e)with the MD simulation (Figure 57) we can see that the model of MD is much more detailed than the normal modes as it is possible to see the motion of the side chains and not only of the domains or secondary structures. Additionally the protein which is simulated by MD shows much more motion in the whole cell and does not seem to be sticked at one position.<br></div></td>
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<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>When we compare the MD simulation with the mode 7 of WEBnm@ we can observe that both show the motion of the end of the protein (right side in MD and left side in WEBnm@) which is very similar in both cases. But we have to see that only the general movement is very similar since there is a lot of flexibility inside of the structure in the MD simulation which is not shown in the model of the WEBnm@. There is also motion in the other end of the protein which is also displayed by both simulation tools but in two different kinds of movement. In the MD simulation it seems like the red colored end of the protein folds away of the protein and returns to it again. Contrary in the WEBnm@ the end seems to be always a bit away of the rest of the protein and just sways a bit up and down.<br></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>When we compare the MD simulation with the mode 7 of WEBnm@ we can observe that both show the motion of the end of the protein (right side in MD and left side in WEBnm@) which is very similar in both cases. But we have to see that only the general movement is very similar since there is a lot of flexibility inside of the structure in the MD simulation which is not shown in the model of the WEBnm@. There is also motion in the other end of the protein which is also displayed by both simulation tools but in two different kinds of movement. In the MD simulation it seems like the red colored end of the protein folds away of the protein and returns to it again. Contrary in the WEBnm@ the end seems to be always a bit away of the rest of the protein and just sways a bit up and down.<br></div></td>
</tr>
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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 7 of ElNemo has the same problem as WEBnm@. It also shows that there is motion in the end of the protein (left side) but again this motion is very <del class="diffchange diffchange-inline">simple displayed</del>. It seems like the end of the protein becks but as we can see in the visualisation of the MD simulation<del class="diffchange diffchange-inline"> that</del> this is just a rough estimate of the movement. The more detailed motion is very flexible and moves in all directions. One very interesting observation in Figure 56b is that there is a small part in the center of the protein which is very flexible and becks up and down. This is not shown in the MD simulation and also in no other normal modes so we are not sure if this is really a flexible part of the protein. The next difference between the ElNemo model and the protein of the MD simulation is that there is no motion of the end of the protein shown in the model while there is a lot of movement in Figure 57.<br></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 7 of ElNemo has the same problem as WEBnm@. It also shows that there is motion in the end of the protein (left side) but again this motion is<ins class="diffchange diffchange-inline"> displayed</ins> very <ins class="diffchange diffchange-inline">simplified</ins>. It seems like the end of the protein becks but as we can see in the visualisation of the MD simulation this is just a rough estimate of the movement. The more detailed motion is very flexible and moves in all directions. One very interesting observation in Figure 56b is that there is a small part in the center of the protein which is very flexible and becks up and down. This is not shown in the MD simulation and also in no other normal modes so we are not sure if this is really a flexible part of the protein. The next difference between the ElNemo model and the protein of the MD simulation is that there is no motion of the end of the protein shown in the model while there is a lot of movement<ins class="diffchange diffchange-inline"> in the MD simulation given</ins> in Figure 57.<br></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>By comparing the normal mode 7 produced by ANM with the MD simulation we have again this becking part in the end of the protein as in the WEBnm@ mode which is different to the motion in the end of the protein of the MD. As the end of mode7 the beginning also only goes up and down and <del class="diffchange diffchange-inline">do</del> not move in any other direction so the flexibility of this part is much less than in the MD simulation.<br></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>By comparing the normal mode 7 produced by ANM with the MD simulation we have again this becking part in the end of the protein as in the WEBnm@ mode which is different to the motion in the end of the protein of the MD. As the end of mode7 the beginning also only goes up and down and <ins class="diffchange diffchange-inline">does</ins> not move in any other direction so the flexibility of this part is much less than in the MD simulation.<br></div></td>
</tr>
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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>The normal modes of oGNM are completely different to the MD simulation. Thie program returns no protein but only shows the parts of the protein which are flexible. So we can not say whether the parts move in the same direction or not. But we can see whether the flexible parts are the same. Both proteins are flexible at the one end of the protein (right side in both cases) and since there are many red parts where some are deep red in the model of oGNM it seems that this end is also very flexible. But this is the only similarity between the two proteins. In the MD simulation there is also motion in the other end of the protein which is not the case in mode 8 of oGNM. Contrary to this the light pink parts in the center of the protein indicate that there is motion in these regions which does not occur in the MD simulation.<br></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>The normal modes of oGNM are completely different to the MD simulation. Thie program returns no<ins class="diffchange diffchange-inline"> visualization of a</ins> protein<ins class="diffchange diffchange-inline"> in motion</ins> but only shows the parts of the protein which are flexible. So we can not say whether the parts move in the same direction or not. But we can see whether the flexible parts are the same. Both proteins are flexible at the one end of the protein (right side in both cases) and since there are many red parts where some are deep red in the model of oGNM it seems that this end is also very flexible. But this is the only similarity between the two proteins. In the MD simulation there is also motion in the other end of the protein which is not the case in mode 8 of oGNM. Contrary to this the light pink parts in the center of the protein indicate that there is motion in these regions which does not occur in the MD simulation.<br></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>The model of NOMAD-Ref shows again many differences to the protein of the MD simulation. It seems that the whole protein is fixed except of the end of the protein on the right side of Figure 56e. Contrary to this observation we can see in the visualisation of the protein of the MD that the whole protein moves a bit around in the cell and that there is motion in both ends of the protein. By comparing the movement of the two <del class="diffchange diffchange-inline">end</del> which are <del class="diffchange diffchange-inline">predict</del> to be flexible by both programms we can say that mode 7 of NOMAD-Ref is more similar to the MD simulation than the other NMA tools since there is more motion and flexibility in the structures itself. It does not only go up and down but moves in all directions which is more <del class="diffchange diffchange-inline">likely to</del> the simulated protein. Of course it <del class="diffchange diffchange-inline">is</del> not as <del class="diffchange diffchange-inline">flexible</del> as the protein of the MD simulation since the moving side chains are hidden. <br></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>The model of NOMAD-Ref shows again many differences to the protein of the MD simulation. It seems that the whole protein is fixed except of the end of the protein on the right side of Figure 56e. Contrary to this observation we can see in the visualisation of the protein of the MD that the whole protein moves a bit around in the cell and that there is motion in both ends of the protein. By comparing the movement of the two <ins class="diffchange diffchange-inline">ends</ins> which are <ins class="diffchange diffchange-inline">predicted</ins> to be flexible by both programms we can say that mode 7 of NOMAD-Ref is more similar to the MD simulation than the other NMA tools since there is more motion and flexibility in the structures itself. It does not only go up and down but moves in all directions which is more <ins class="diffchange diffchange-inline">like</ins> the simulated protein. Of course it <ins class="diffchange diffchange-inline">does</ins> not<ins class="diffchange diffchange-inline"> show</ins> as <ins class="diffchange diffchange-inline">much motion</ins> as<ins class="diffchange diffchange-inline"> is</ins> the protein of the MD simulation since the moving side chains are hidden. <br></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>All in all we can say that the general information given by the several tools that there is only motion in the end of the protein is mostly <del class="diffchange diffchange-inline">equal</del> except of some cases where additional <del class="diffchange diffchange-inline">movement</del> in the center of the protein <del class="diffchange diffchange-inline">is</del> predicted. But the detailed information about the movement of the protein like for example the direction is completely different between the MD simulation and the NMA.</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>All in all we can say that the general information given by the several tools that there is only motion in the end of the protein is mostly <ins class="diffchange diffchange-inline">the same</ins> except of some cases where additional <ins class="diffchange diffchange-inline">movements</ins> in the center of the protein <ins class="diffchange diffchange-inline">are</ins> predicted. But the detailed information about the movement of the protein<ins class="diffchange diffchange-inline">,</ins> like for example the direction<ins class="diffchange diffchange-inline">,</ins> is completely different between the MD simulation and the NMA.</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;"></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>
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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>== References ==</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>== References ==</div></td>
</tr>
</table>Demelhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_BCKDHA&diff=15780&oldid=prevReisinger: /* Comparison of the lowest-frequency normal modes with the MD simulation */2011-09-28T13:00:37Z<p><span dir="auto"><span class="autocomment">Comparison of the lowest-frequency normal modes with the MD simulation</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<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 13:00, 28 September 2011</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>Mode 7 of ElNemo has the same problem as WEBnm@. It also shows that there is motion in the end of the protein (left side) but again this motion is very simple displayed. It seems like the end of the protein becks but as we can see in the visualisation of the MD simulation that this is just a rough estimate of the movement. The more detailed motion is very flexible and moves in all directions. One very interesting observation in Figure 56b is that there is a small part in the center of the protein which is very flexible and becks up and down. This is not shown in the MD simulation and also in no other normal modes so we are not sure if this is really a flexible part of the protein. The next difference between the ElNemo model and the protein of the MD simulation is that there is no motion of the end of the protein shown in the model while there is a lot of movement in Figure 57.<br></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 of ElNemo has the same problem as WEBnm@. It also shows that there is motion in the end of the protein (left side) but again this motion is very simple displayed. It seems like the end of the protein becks but as we can see in the visualisation of the MD simulation that this is just a rough estimate of the movement. The more detailed motion is very flexible and moves in all directions. One very interesting observation in Figure 56b is that there is a small part in the center of the protein which is very flexible and becks up and down. This is not shown in the MD simulation and also in no other normal modes so we are not sure if this is really a flexible part of the protein. The next difference between the ElNemo model and the protein of the MD simulation is that there is no motion of the end of the protein shown in the model while there is a lot of movement in Figure 57.<br></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>By comparing the normal mode 7 produced by ANM with the MD simulation we have again this becking part in the end of the protein as in the WEBnm@ mode which is different to the motion in the end of the protein of the MD. As the end of mode7 the beginning also only goes up and down and do not move in any other direction so the flexibility of this part is much less than in the MD simulation.<br></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>By comparing the normal mode 7 produced by ANM with the MD simulation we have again this becking part in the end of the protein as in the WEBnm@ mode which is different to the motion in the end of the protein of the MD. As the end of mode7 the beginning also only goes up and down and do not move in any other direction so the flexibility of this part is much less than in the MD simulation.<br></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>The normal modes of oGNM are completely different to the MD simulation. Thie program returns no protein but only shows the parts of the protein which are flexible. So we can not say whether the parts move in the same direction or not. But we can see whether the flexible parts are the same. Both proteins are flexible at the one end of the protein (right side in both cases) and since there are many red parts where some are deep red in the model of oGNM it seems that this end is also very flexible. But this is the only similarity between the two proteins. In the MD simulation there is also motion in the other end of the protein which is not the case in mode 8 of oGNM. Contrary to this the light pink parts in the center of the protein indicate that there is motion in these regions which does not occur in the MD simulation.</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>The normal modes of oGNM are completely different to the MD simulation. Thie program returns no protein but only shows the parts of the protein which are flexible. So we can not say whether the parts move in the same direction or not. But we can see whether the flexible parts are the same. Both proteins are flexible at the one end of the protein (right side in both cases) and since there are many red parts where some are deep red in the model of oGNM it seems that this end is also very flexible. But this is the only similarity between the two proteins. In the MD simulation there is also motion in the other end of the protein which is not the case in mode 8 of oGNM. Contrary to this the light pink parts in the center of the protein indicate that there is motion in these regions which does not occur in the MD simulation.<ins class="diffchange diffchange-inline"><br></ins></div></td>
</tr>
<tr>
<td colspan="2" class="diff-empty"> </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>The model of NOMAD-Ref shows again many differences to the protein of the MD simulation. It seems that the whole protein is fixed except of the end of the protein on the right side of Figure 56e. Contrary to this observation we can see in the visualisation of the protein of the MD that the whole protein moves a bit around in the cell and that there is motion in both ends of the protein. By comparing the movement of the two end which are predict to be flexible by both programms we can say that mode 7 of NOMAD-Ref is more similar to the MD simulation than the other NMA tools since there is more motion and flexibility in the structures itself. It does not only go up and down but moves in all directions which is more likely to the simulated protein. Of course it is not as flexible as the protein of the MD simulation since the moving side chains are hidden. <br></div></td>
</tr>
<tr>
<td colspan="2" class="diff-empty"> </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>All in all we can say that the general information given by the several tools that there is only motion in the end of the protein is mostly equal except of some cases where additional movement in the center of the protein is predicted. But the detailed information about the movement of the protein like for example the direction is completely different between the MD simulation and the NMA.</div></td>
</tr>
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<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>
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<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>== References ==</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>== References ==</div></td>
</tr>
</table>Reisingerhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_BCKDHA&diff=15779&oldid=prevReisinger: /* Comparison of the lowest-frequency normal modes with the MD simulation */2011-09-28T12:46:55Z<p><span dir="auto"><span class="autocomment">Comparison of the lowest-frequency normal modes with the MD simulation</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<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 12:46, 28 September 2011</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:BCKDHA_ANM_mode7.gif|thumb|200px|Figure56c: ANM: mode 7]]</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:BCKDHA_ANM_mode7.gif|thumb|200px|Figure56c: ANM: mode 7]]</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: OGNM_mode8_visualization_BCKDHA.png|thumb|253px|Figure56d: oGNM: 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>||[[File: OGNM_mode8_visualization_BCKDHA.png|thumb|253px|Figure56d: oGNM: mode 8]]</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>|| [[Image:BCKDHA_NOMAD_mode7.gif|thumb|200px|Figure56e: NOMAD: mode 7]]</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>|| [[Image:BCKDHA_NOMAD_mode7.gif|thumb|200px|Figure56e: NOMAD<ins class="diffchange diffchange-inline">-Ref</ins>: mode 7]]</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>|}</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>|}</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><br><br></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><br></div></td>
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</table>Reisingerhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_BCKDHA&diff=15778&oldid=prevReisinger: /* Comparison of the lowest-frequency normal modes with the MD simulation */2011-09-28T12:30:04Z<p><span dir="auto"><span class="autocomment">Comparison of the lowest-frequency normal modes with the MD simulation</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
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<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 12:30, 28 September 2011</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:Mod7_1_BCKDHA.gif|thumb|150px|Figure56b: ElNemo: 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>|| [[File:Mod7_1_BCKDHA.gif|thumb|150px|Figure56b: ElNemo: mode 7]]</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:BCKDHA_ANM_mode7.gif|thumb|200px|Figure56c: ANM: 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>|| [[File:BCKDHA_ANM_mode7.gif|thumb|200px|Figure56c: ANM: mode 7]]</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>||<del class="diffchange diffchange-inline"> </del>[[File: <del class="diffchange diffchange-inline">OGNM_mode7_visualization_BCKDHA</del>.png|thumb|<del class="diffchange diffchange-inline">225px</del>|Figure56d: oGNM: mode <del class="diffchange diffchange-inline">7</del>]]</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>||[[File: <ins class="diffchange diffchange-inline">OGNM_mode8_visualization_BCKDHA</ins>.png|thumb|<ins class="diffchange diffchange-inline">253px</ins>|Figure56d: oGNM: mode <ins class="diffchange diffchange-inline">8</ins>]]</div></td>
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<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>|| [[Image:BCKDHA_NOMAD_mode7.gif|thumb|200px|Figure56e: NOMAD: 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>|| [[Image:BCKDHA_NOMAD_mode7.gif|thumb|200px|Figure56e: NOMAD: mode 7]]</div></td>
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<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>|}</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>|}</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>When we compare the MD simulation with the mode 7 of WEBnm@ we can observe that both show the motion of the end of the protein (right side in MD and left side in WEBnm@) which is very similar in both cases. But we have to see that only the general movement is very similar since there is a lot of flexibility inside of the structure in the MD simulation which is not shown in the model of the WEBnm@. There is also motion in the other end of the protein which is also displayed by both simulation tools but in two different kinds of movement. In the MD simulation it seems like the red colored end of the protein folds away of the protein and returns to it again. Contrary in the WEBnm@ the end seems to be always a bit away of the rest of the protein and just sways a bit up and down.<br></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>When we compare the MD simulation with the mode 7 of WEBnm@ we can observe that both show the motion of the end of the protein (right side in MD and left side in WEBnm@) which is very similar in both cases. But we have to see that only the general movement is very similar since there is a lot of flexibility inside of the structure in the MD simulation which is not shown in the model of the WEBnm@. There is also motion in the other end of the protein which is also displayed by both simulation tools but in two different kinds of movement. In the MD simulation it seems like the red colored end of the protein folds away of the protein and returns to it again. Contrary in the WEBnm@ the end seems to be always a bit away of the rest of the protein and just sways a bit up and down.<br></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 7 of ElNemo has the same problem as WEBnm@. It also shows that there is motion in the end of the protein (left side) but again this motion is very simple displayed. It seems like the end of the protein becks but as we can see in the visualisation of the MD simulation that this is just a rough estimate of the movement. The more detailed motion is very flexible and moves in all directions. One very interesting observation in Figure 56b is that there is a small part in the center of the protein which is very flexible and becks up and down. This is not shown in the MD simulation and also in no other normal modes so we are not sure if this is really a flexible part of the protein. The next difference between the ElNemo model and the protein of the MD simulation is that there is no motion of the end of the protein shown in the model while there is a lot of movement in Figure 57.<br></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 of ElNemo has the same problem as WEBnm@. It also shows that there is motion in the end of the protein (left side) but again this motion is very simple displayed. It seems like the end of the protein becks but as we can see in the visualisation of the MD simulation that this is just a rough estimate of the movement. The more detailed motion is very flexible and moves in all directions. One very interesting observation in Figure 56b is that there is a small part in the center of the protein which is very flexible and becks up and down. This is not shown in the MD simulation and also in no other normal modes so we are not sure if this is really a flexible part of the protein. The next difference between the ElNemo model and the protein of the MD simulation is that there is no motion of the end of the protein shown in the model while there is a lot of movement in Figure 57.<br></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>By comparing the normal mode 7 produced by ANM with the MD simulation we have again this becking part in the end of the protein as in the WEBnm@ mode which is different to the motion in the end of the protein of the MD. As the end of mode7 the beginning also only goes up and down and do not move in any other direction so the flexibility of this part is much less than in the MD simulation.</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>By comparing the normal mode 7 produced by ANM with the MD simulation we have again this becking part in the end of the protein as in the WEBnm@ mode which is different to the motion in the end of the protein of the MD. As the end of mode7 the beginning also only goes up and down and do not move in any other direction so the flexibility of this part is much less than in the MD simulation.<ins class="diffchange diffchange-inline"><br></ins></div></td>
</tr>
<tr>
<td colspan="2" class="diff-empty"> </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>The normal modes of oGNM are completely different to the MD simulation. Thie program returns no protein but only shows the parts of the protein which are flexible. So we can not say whether the parts move in the same direction or not. But we can see whether the flexible parts are the same. Both proteins are flexible at the one end of the protein (right side in both cases) and since there are many red parts where some are deep red in the model of oGNM it seems that this end is also very flexible. But this is the only similarity between the two proteins. In the MD simulation there is also motion in the other end of the protein which is not the case in mode 8 of oGNM. Contrary to this the light pink parts in the center of the protein indicate that there is motion in these regions which does not occur in the MD simulation.</div></td>
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<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>== References ==</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>== References ==</div></td>
</tr>
</table>Reisingerhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_BCKDHA&diff=15777&oldid=prevReisinger: /* Comparison of the lowest-frequency normal modes with the MD simulation */2011-09-28T12:17:07Z<p><span dir="auto"><span class="autocomment">Comparison of the lowest-frequency normal modes with the MD simulation</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
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<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 12:17, 28 September 2011</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;"></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>
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<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>By comparing the normal modes (Figure 56a-e)with the MD simulation (Figure 57) we can see that the model of MD is much more detailed than the normal modes as it is possible to see the motion of the side chains and not only of the domains or secondary structures. Additionally the protein which is simulated by MD shows much more motion in the whole cell and does not seem to be sticked at one position.<br></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>By comparing the normal modes (Figure 56a-e)with the MD simulation (Figure 57) we can see that the model of MD is much more detailed than the normal modes as it is possible to see the motion of the side chains and not only of the domains or secondary structures. Additionally the protein which is simulated by MD shows much more motion in the whole cell and does not seem to be sticked at one position.<br></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>When we compare the MD simulation with the mode 7 of WEBnm@ we can observe that both show the motion of the end of the protein (right side in MD and left side in WEBnm@) which is very similar in both cases. But we have to see that only the general movement is very similar since there is a lot of flexibility inside of the structure in the MD simulation which is not shown in the model of the WEBnm@. There is also motion in the other end of the protein which is also displayed by both simulation tools but in two different kinds of movement. In the MD simulation it seems like the red colored end of the protein folds away of the protein and returns to it again. Contrary in the WEBnm@ the end seems to be always a bit away of the rest of the protein and just sways a bit up and down.</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>When we compare the MD simulation with the mode 7 of WEBnm@ we can observe that both show the motion of the end of the protein (right side in MD and left side in WEBnm@) which is very similar in both cases. But we have to see that only the general movement is very similar since there is a lot of flexibility inside of the structure in the MD simulation which is not shown in the model of the WEBnm@. There is also motion in the other end of the protein which is also displayed by both simulation tools but in two different kinds of movement. In the MD simulation it seems like the red colored end of the protein folds away of the protein and returns to it again. Contrary in the WEBnm@ the end seems to be always a bit away of the rest of the protein and just sways a bit up and down.<ins class="diffchange diffchange-inline"><br></ins></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>Mode 7 of ElNemo has the same problem as WEBnm@. It also shows that there is motion in the end of the protein (left side) but again this motion is very simple displayed. It seems like the end of the protein becks but as we can see in the visualisation of the MD simulation that this is just a rough estimate of the movement. The more detailed motion is very flexible and moves in all directions. One very interesting observation in Figure 56b is that there is a small part in the center of the protein which is very flexible and becks up and down. This is not shown in the MD simulation and also in no other normal modes so we are not sure if this is really a flexible part of the protein. The next difference between the ElNemo model and the protein of the MD simulation is that there is no motion of the end of the protein shown in the model while there is a lot of movement in Figure 57.</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 7 of ElNemo has the same problem as WEBnm@. It also shows that there is motion in the end of the protein (left side) but again this motion is very simple displayed. It seems like the end of the protein becks but as we can see in the visualisation of the MD simulation that this is just a rough estimate of the movement. The more detailed motion is very flexible and moves in all directions. One very interesting observation in Figure 56b is that there is a small part in the center of the protein which is very flexible and becks up and down. This is not shown in the MD simulation and also in no other normal modes so we are not sure if this is really a flexible part of the protein. The next difference between the ElNemo model and the protein of the MD simulation is that there is no motion of the end of the protein shown in the model while there is a lot of movement in Figure 57.<ins class="diffchange diffchange-inline"><br></ins></div></td>
</tr>
<tr>
<td colspan="2" class="diff-empty"> </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>By comparing the normal mode 7 produced by ANM with the MD simulation we have again this becking part in the end of the protein as in the WEBnm@ mode which is different to the motion in the end of the protein of the MD. As the end of mode7 the beginning also only goes up and down and do not move in any other direction so the flexibility of this part is much less than in the MD simulation.</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>== References ==</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>== References ==</div></td>
</tr>
</table>Reisingerhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_BCKDHA&diff=15775&oldid=prevReisinger: /* Comparison of the lowest-frequency normal modes with the MD simulation */2011-09-28T11:13:38Z<p><span dir="auto"><span class="autocomment">Comparison of the lowest-frequency normal modes with the MD simulation</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 11:13, 28 September 2011</td>
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<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>By comparing the normal modes (Figure 56a-e)with the MD simulation (Figure 57) we can see that the model of MD is much more detailed than the normal modes as it is possible to see the motion of the side chains and not only of the domains or secondary structures. Additionally the protein which is simulated by MD shows much more motion in the whole cell and does not seem to be sticked at one position.<br></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>By comparing the normal modes (Figure 56a-e)with the MD simulation (Figure 57) we can see that the model of MD is much more detailed than the normal modes as it is possible to see the motion of the side chains and not only of the domains or secondary structures. Additionally the protein which is simulated by MD shows much more motion in the whole cell and does not seem to be sticked at one position.<br></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>When we compare the MD simulation with the mode 7 of WEBnm@ we can observe that both show the motion of the end of the protein (right side in MD and left side in WEBnm@) which is very similar in both cases. But we have to see that only the general movement is very similar since there is a lot of flexibility inside of the structure in the MD simulation which is not shown in the model of the WEBnm@. There is also motion in the other end of the protein which is also displayed by both simulation tools but in two different kinds of movement. In the MD simulation it seems like the red colored end of the protein folds away of the protein and returns to it again. Contrary in the WEBnm@ the end seems to be always a bit away of the rest of the protein and just sways a bit up and down.</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>When we compare the MD simulation with the mode 7 of WEBnm@ we can observe that both show the motion of the end of the protein (right side in MD and left side in WEBnm@) which is very similar in both cases. But we have to see that only the general movement is very similar since there is a lot of flexibility inside of the structure in the MD simulation which is not shown in the model of the WEBnm@. There is also motion in the other end of the protein which is also displayed by both simulation tools but in two different kinds of movement. In the MD simulation it seems like the red colored end of the protein folds away of the protein and returns to it again. Contrary in the WEBnm@ the end seems to be always a bit away of the rest of the protein and just sways a bit up and down.</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>Mode 7 of ElNemo has the same problem as WEBnm@. It also shows that there is motion in the end of the protein (left side) but again this motion is very simple displayed. It seems like the end of the protein becks but as we can see in the visualisation of the MD simulation this is just a rough estimate of the movement. The more detailed motion is very flexible and moves in all directions.</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 7 of ElNemo has the same problem as WEBnm@. It also shows that there is motion in the end of the protein (left side) but again this motion is very simple displayed. It seems like the end of the protein becks but as we can see in the visualisation of the MD simulation<ins class="diffchange diffchange-inline"> that</ins> this is just a rough estimate of the movement. The more detailed motion is very flexible and moves in all directions<ins class="diffchange diffchange-inline">. One very interesting observation in Figure 56b is that there is a small part in the center of the protein which is very flexible and becks up and down. This is not shown in the MD simulation and also in no other normal modes so we are not sure if this is really a flexible part of the protein. The next difference between the ElNemo model and the protein of the MD simulation is that there is no motion of the end of the protein shown in the model while there is a lot of movement in Figure 57</ins>.</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>== References ==</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>== References ==</div></td>
</tr>
</table>Reisingerhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_BCKDHA&diff=15774&oldid=prevReisinger: /* Comparison of the lowest-frequency normal modes with the MD simulation */2011-09-28T10:54:00Z<p><span dir="auto"><span class="autocomment">Comparison of the lowest-frequency normal modes with the MD simulation</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 10:54, 28 September 2011</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 533:</td>
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<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>By comparing the normal modes (Figure 56a-e)with the MD simulation (Figure 57) we can see that the model of MD is much more detailed than the normal modes as it is possible to see the motion of the side chains and not only of the domains or secondary structures. Additionally the protein which is simulated by MD shows much more motion in the whole cell and does not seem to be sticked at one position.<br></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>By comparing the normal modes (Figure 56a-e)with the MD simulation (Figure 57) we can see that the model of MD is much more detailed than the normal modes as it is possible to see the motion of the side chains and not only of the domains or secondary structures. Additionally the protein which is simulated by MD shows much more motion in the whole cell and does not seem to be sticked at one position.<br></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>When we compare the MD simulation with the mode 7 of WEBnm@ we can observe that both show the motion of the end of the protein (right side in MD and left side in WEBnm@) which is very similar in both cases. But we have to see that only the general movement is very similar since there is a lot of flexibility inside of the structure in the MD simulation which is not shown in the model of the WEBnm@. There is also motion in the other end of the protein which is also displayed by both simulation tools but in two different kinds of movement. In the MD simulation it seems like the red colored end of the protein folds away of the protein and returns to it again. Contrary in the WEBnm@ the end seems to be always a bit away of the rest of the protein and just sways a bit up and down.</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>When we compare the MD simulation with the mode 7 of WEBnm@ we can observe that both show the motion of the end of the protein (right side in MD and left side in WEBnm@) which is very similar in both cases. But we have to see that only the general movement is very similar since there is a lot of flexibility inside of the structure in the MD simulation which is not shown in the model of the WEBnm@. There is also motion in the other end of the protein which is also displayed by both simulation tools but in two different kinds of movement. In the MD simulation it seems like the red colored end of the protein folds away of the protein and returns to it again. Contrary in the WEBnm@ the end seems to be always a bit away of the rest of the protein and just sways a bit up and down.</div></td>
</tr>
<tr>
<td colspan="2" class="diff-empty"> </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 7 of ElNemo has the same problem as WEBnm@. It also shows that there is motion in the end of the protein (left side) but again this motion is very simple displayed. It seems like the end of the protein becks but as we can see in the visualisation of the MD simulation this is just a rough estimate of the movement. The more detailed motion is very flexible and moves in all directions.</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>== References ==</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>== References ==</div></td>
</tr>
</table>Reisingerhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_BCKDHA&diff=15773&oldid=prevReisinger: /* Comparison of the lowest-frequency normal modes with the MD simulation */2011-09-28T10:46:21Z<p><span dir="auto"><span class="autocomment">Comparison of the lowest-frequency normal modes with the MD simulation</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 10:46, 28 September 2011</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;"></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>By comparing the normal modes (Figure 56a-e)with the MD simulation (Figure 57) we can see that the model of MD is much more detailed than the normal modes as it is possible to see the motion of the side chains and not only of the domains or secondary structures. Additionally the protein which is simulated by MD shows much more motion in the whole cell and does not seem to be sticked at one position.<br></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>By comparing the normal modes (Figure 56a-e)with the MD simulation (Figure 57) we can see that the model of MD is much more detailed than the normal modes as it is possible to see the motion of the side chains and not only of the domains or secondary structures. Additionally the protein which is simulated by MD shows much more motion in the whole cell and does not seem to be sticked at one position.<br></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>When we compare the MD simulation with the mode 7 of WEBnm@ we can observe that both show the motion of the end of the protein (right side in MD and left side in WEBnm@) which is very similar in both cases. But we have to see that only the general movement is very similar since there is a lot of flexibility inside of the structure in the MD simulation which is not shown in the model of the WEBnm@.</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>When we compare the MD simulation with the mode 7 of WEBnm@ we can observe that both show the motion of the end of the protein (right side in MD and left side in WEBnm@) which is very similar in both cases. But we have to see that only the general movement is very similar since there is a lot of flexibility inside of the structure in the MD simulation which is not shown in the model of the WEBnm@<ins class="diffchange diffchange-inline">. There is also motion in the other end of the protein which is also displayed by both simulation tools but in two different kinds of movement. In the MD simulation it seems like the red colored end of the protein folds away of the protein and returns to it again. Contrary in the WEBnm@ the end seems to be always a bit away of the rest of the protein and just sways a bit up and down</ins>.</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>== References ==</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>== References ==</div></td>
</tr>
</table>Reisingerhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_BCKDHA&diff=15772&oldid=prevReisinger: /* Comparison of the lowest-frequency normal modes with the MD simulation */2011-09-28T10:40:24Z<p><span dir="auto"><span class="autocomment">Comparison of the lowest-frequency normal modes with the MD simulation</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 10:40, 28 September 2011</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>!NOMAD-Ref</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>!NOMAD-Ref</div></td>
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<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>|-</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>|-</div></td>
</tr>
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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>|[[File:<del class="diffchange diffchange-inline">Mod7_BCKDHA</del>.gif<del class="diffchange diffchange-inline"> </del>| thumb |200px| Figure56a: WEBnm@: mode <del class="diffchange diffchange-inline">7</del>]]<del class="diffchange diffchange-inline"> </del></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>|[[File:<ins class="diffchange diffchange-inline">Mod11_BCKDHA</ins>.gif| thumb |200px| Figure56a: WEBnm@: mode <ins class="diffchange diffchange-inline">11</ins>]]</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>|| [[File:Mod7_1_BCKDHA.gif|thumb|150px|Figure56b: ElNemo: 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>|| [[File:Mod7_1_BCKDHA.gif|thumb|150px|Figure56b: ElNemo: 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>|| [[File:BCKDHA_ANM_mode7.gif|thumb|200px|Figure56c: ANM: 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>|| [[File:BCKDHA_ANM_mode7.gif|thumb|200px|Figure56c: ANM: mode 7]]</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;"></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>By comparing the normal modes (Figure 56a-e)with the MD simulation (Figure 57) we can see that the model of MD is much more detailed than the normal modes as it is possible to see the motion of the side chains and not only of the domains or secondary structures. Additionally the protein which is simulated by MD shows much more motion in the whole cell and does not seem to be sticked at one position.<br></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>By comparing the normal modes (Figure 56a-e)with the MD simulation (Figure 57) we can see that the model of MD is much more detailed than the normal modes as it is possible to see the motion of the side chains and not only of the domains or secondary structures. Additionally the protein which is simulated by MD shows much more motion in the whole cell and does not seem to be sticked at one position.<br></div></td>
</tr>
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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>When we compare the MD simulation with the mode 7 of WEBnm@ we can observe that both show the motion of the end of the protein (right side in MD and left side in WEBnm@)<del class="diffchange diffchange-inline">.</del> <del class="diffchange diffchange-inline">But there</del> is <del class="diffchange diffchange-inline">a</del> <del class="diffchange diffchange-inline">difference</del> in <del class="diffchange diffchange-inline">the</del> <del class="diffchange diffchange-inline">motion</del>. <del class="diffchange diffchange-inline">While</del> <del class="diffchange diffchange-inline">it</del> <del class="diffchange diffchange-inline">moves</del> <del class="diffchange diffchange-inline">around</del> <del class="diffchange diffchange-inline">the</del> <del class="diffchange diffchange-inline">whole left side of the protein in the normal mode it</del> only<del class="diffchange diffchange-inline"> ranges between</del> the <del class="diffchange diffchange-inline">right</del> <del class="diffchange diffchange-inline">middle</del> <del class="diffchange diffchange-inline">and</del> <del class="diffchange diffchange-inline">the</del> <del class="diffchange diffchange-inline">bottom</del> <del class="diffchange diffchange-inline">right part of the protein in the MD so</del> there is <del class="diffchange diffchange-inline">more</del> <del class="diffchange diffchange-inline">movement</del> of<del class="diffchange diffchange-inline"> the whole end of the protein. Contrary to this observation we can say that there is no</del> flexibility inside of the structure in the <del class="diffchange diffchange-inline">model</del> <del class="diffchange diffchange-inline">of</del> <del class="diffchange diffchange-inline">NMD but there</del> is <del class="diffchange diffchange-inline">a lot flexibility</del> shown in the <del class="diffchange diffchange-inline">MD</del> <del class="diffchange diffchange-inline">simulation</del>.</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>When we compare the MD simulation with the mode 7 of WEBnm@ we can observe that both show the motion of the end of the protein (right side in MD and left side in WEBnm@) <ins class="diffchange diffchange-inline">which</ins> is <ins class="diffchange diffchange-inline">very</ins> <ins class="diffchange diffchange-inline">similar</ins> in <ins class="diffchange diffchange-inline">both</ins> <ins class="diffchange diffchange-inline">cases</ins>. <ins class="diffchange diffchange-inline">But</ins> <ins class="diffchange diffchange-inline">we</ins> <ins class="diffchange diffchange-inline">have</ins> <ins class="diffchange diffchange-inline">to</ins> <ins class="diffchange diffchange-inline">see</ins> <ins class="diffchange diffchange-inline">that</ins> only the <ins class="diffchange diffchange-inline">general</ins> <ins class="diffchange diffchange-inline">movement</ins> <ins class="diffchange diffchange-inline">is</ins> <ins class="diffchange diffchange-inline">very</ins> <ins class="diffchange diffchange-inline">similar</ins> <ins class="diffchange diffchange-inline">since</ins> there is <ins class="diffchange diffchange-inline">a</ins> <ins class="diffchange diffchange-inline">lot</ins> of flexibility inside of the structure in the <ins class="diffchange diffchange-inline">MD</ins> <ins class="diffchange diffchange-inline">simulation</ins> <ins class="diffchange diffchange-inline">which</ins> is <ins class="diffchange diffchange-inline">not</ins> shown in the <ins class="diffchange diffchange-inline">model</ins> <ins class="diffchange diffchange-inline">of the WEBnm@</ins>.</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>== References ==</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>== References ==</div></td>
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</table>Reisingerhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_BCKDHA&diff=15771&oldid=prevReisinger: /* Comparison of the lowest-frequency normal modes with the MD simulation */2011-09-28T10:30:04Z<p><span dir="auto"><span class="autocomment">Comparison of the lowest-frequency normal modes with the MD simulation</span></span></p>
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<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 10:30, 28 September 2011</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;"></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>By comparing the normal modes with the MD simulation we can see that the model of MD is much more detailed than the normal modes as it is possible to see the motion of the side chains and not only of the domains or secondary structures.</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>By comparing the normal modes <ins class="diffchange diffchange-inline">(Figure 56a-e)</ins>with the MD simulation<ins class="diffchange diffchange-inline"> (Figure 57)</ins> we can see that the model of MD is much more detailed than the normal modes as it is possible to see the motion of the side chains and not only of the domains or secondary structures.<ins class="diffchange diffchange-inline"> Additionally the protein which is simulated by MD shows much more motion in the whole cell and does not seem to be sticked at one position.<br></ins></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>When we compare the MD simulation with the mode 7 of WEBnm@ we can observe that both show the motion of the end of the protein (right side in MD and left side in WEBnm@). But there is a difference in the motion. While it moves around the whole left side of the protein in the normal mode it only ranges between the right middle and the bottom right part of the protein in the MD so there is more movement of the whole end of the protein. Contrary to this observation we can say that there is no flexibility inside of the structure in the model of NMD but there is a lot flexibility shown in the MD simulation.</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>== References ==</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>== References ==</div></td>
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</table>Reisinger