https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_of_ARSA&feed=atom&action=historyNormal Mode Analysis of ARSA - Revision history2024-03-29T02:10:41ZRevision history for this page on the wikiMediaWiki 1.31.16https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_of_ARSA&diff=16089&oldid=prevAndrea: /* References */2012-03-29T13:01:03Z<p><span dir="auto"><span class="autocomment">References</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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[[Category : Metachromatic_Leukodystrophy]]</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>[[Category : Metachromatic_Leukodystrophy<ins class="diffchange diffchange-inline"> 2011</ins>]]</div></td>
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</table>Andreahttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_of_ARSA&diff=15761&oldid=prevZacher at 22:07, 27 September 20112011-09-27T22:07:17Z<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>We have applied five different methods to calculate normal modes for ARSA. Recurent movements are reported by all methods. A large movement of the terminal helix in the protein can be found in the results of each method. Sometimes this helix is involved in an open-close movement around the site where the substrate enters the enzyme. In other modes only the loop region around the cleft is moving. We conclude, that this movements might be functional and could be induced upon substrate binding of the enzyme. However, this hypothesis remains highly speculative, as we do not have any resolved substrate-bound structures of the enzyme. <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>We have applied five different methods to calculate normal modes for ARSA. Recurent movements are reported by all methods. A large movement of the terminal helix in the protein can be found in the results of each method. Sometimes this helix is involved in an open-close movement around the site where the substrate enters the enzyme. In other modes only the loop region around the cleft is moving. We conclude, that this movements might be functional and could be induced upon substrate binding of the enzyme. However, this hypothesis remains highly speculative, as we do not have any resolved substrate-bound structures of the enzyme. <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>These results are reproducible, as all methods output very similar results. No matter, if the movements are functional or not, the results suggest that these parts of the protein - the terminal helix and the loops around the cleft - are important flexible regions in the structure.</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>These results are reproducible, as all methods output very similar results. No matter, if the movements are functional or not, the results suggest that these parts of the protein - the terminal helix and the loops around the cleft - are important flexible regions in the structure.</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><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>[[Category : Metachromatic_Leukodystrophy]]</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>[[Category : Metachromatic_Leukodystrophy]]</div></td>
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</table>Zacherhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_of_ARSA&diff=11106&oldid=prevKassner at 14:23, 14 August 20112011-08-14T14:23:42Z<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>We have applied five different methods to calculate normal modes for ARSA. Recurent movements are reported by all methods. A large movement of the terminal helix in the protein can be found in the results of each method. Sometimes this helix is involved in an open-close movement around the site where the substrate enters the enzyme. In other modes only the loop region around the cleft is moving. We conclude, that this movements might be functional and could be induced upon substrate binding of the enzyme. However, this hypothesis remains highly speculative, as we do not have any resolved substrate-bound structures of the enzyme. <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>We have applied five different methods to calculate normal modes for ARSA. Recurent movements are reported by all methods. A large movement of the terminal helix in the protein can be found in the results of each method. Sometimes this helix is involved in an open-close movement around the site where the substrate enters the enzyme. In other modes only the loop region around the cleft is moving. We conclude, that this movements might be functional and could be induced upon substrate binding of the enzyme. However, this hypothesis remains highly speculative, as we do not have any resolved substrate-bound structures of the enzyme. <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>These results are reproducible, as all methods output very similar results. No matter, if the movements are functional or not, the results suggest that these parts of the protein - the terminal helix and the loops around the cleft - are important flexible regions in the structure.</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>These results are reproducible, as all methods output very similar results. No matter, if the movements are functional or not, the results suggest that these parts of the protein - the terminal helix and the loops around the cleft - are important flexible regions in the structure.</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;"></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>[[Category : Metachromatic_Leukodystrophy]]</div></td>
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</table>Kassnerhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_of_ARSA&diff=11004&oldid=prevZacher: /* Discussion */2011-08-12T14:46:53Z<p><span dir="auto"><span class="autocomment">Discussion</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;"></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>We have applied five different methods to calculate normal modes for ARSA. Recurent movements are reported by all methods. A large movement of the terminal helix in the protein can be found in the results of each method. Sometimes this helix is involved in an open-close movement around the site where the substrate enters the enzyme. In other modes only the loop region around the cleft is moving. We conclude, that this movements might be functional and could be induced upon substrate binding of the enzyme. However, this hypothesis remains highly speculative, as we do not have any resolved substrate-bound structures of the enzyme. <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>We have applied five different methods to calculate normal modes for ARSA. Recurent movements are reported by all methods. A large movement of the terminal helix in the protein can be found in the results of each method. Sometimes this helix is involved in an open-close movement around the site where the substrate enters the enzyme. In other modes only the loop region around the cleft is moving. We conclude, that this movements might be functional and could be induced upon substrate binding of the enzyme. However, this hypothesis remains highly speculative, as we do not have any resolved substrate-bound structures of the enzyme. <br></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>These results are reproducible, as all methods output very similar results. No matter, if the movements are functional or not, the results suggest that these parts of the protein - the terminal helix and the loops around the cleft - are important flexible regions in the structure.</div></td>
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</table>Zacherhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_of_ARSA&diff=11001&oldid=prevZacher: /* Discussion */2011-08-12T14:43:56Z<p><span dir="auto"><span class="autocomment">Discussion</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;"></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>== Discussion ==</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>== Discussion ==</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;"></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>We have applied five different methods to calculate normal modes for ARSA. Recurent movements are reported by all methods. A large movement of the terminal helix in the protein can be found in the results of each method. Sometimes this helix is involved in an open-close movement around the site where the substrate enters the enzyme. In other modes only the loop region around the cleft is moving. We conclude, that this movements might be functional and could be induced upon substrate binding of the enzyme. However, this hypothesis remains highly speculative, as we do not have any resolved substrate-bound structures of the enzyme. <br></div></td>
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</table>Zacherhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_of_ARSA&diff=10999&oldid=prevZacher: /* NOMAD-Ref */2011-08-12T14:39:02Z<p><span dir="auto"><span class="autocomment">NOMAD-Ref</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 14:39, 12 August 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>The results of the all-atom calculation look very similar. As expected the modes, which were calculated at higher temperature show bigger movements compared to the lower temeperature. <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>The results of the all-atom calculation look very similar. As expected the modes, which were calculated at higher temperature show bigger movements compared to the lower temeperature. <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>We tried to compute the modes for the elastic network several times, but we got always the same spurious results, shown in the table above. Somehow, in all modes big unrealistic movements appear. We have removed all solvent atoms using repairPDB, so there should not be any molecules in the pdb causing these effects, so we do not have an explanation, what could have caused this effect. Especially as the all-atom calculations look very nice.</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>We tried to compute the modes for the elastic network several times, but we got always the same spurious results, shown in the table above. Somehow, in all modes big unrealistic movements appear. We have removed all solvent atoms using repairPDB, so there should not be any molecules in the pdb causing these effects, so we do not have an explanation, what could have caused this effect. Especially as the all-atom calculations look very nice.</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;"></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>== Discussion ==</div></td>
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</table>Zacherhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_of_ARSA&diff=10998&oldid=prevZacher: /* NMA of 1BPT */2011-08-12T14:38:13Z<p><span dir="auto"><span class="autocomment">NMA of 1BPT</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;"></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>=== NMA of 1BPT ===</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>=== NMA of 1BPT ===</div></td>
</tr>
<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: #a3d3ff; vertical-align: top; white-space: pre-wrap;"></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>Additional to the elastic network calculation, the Nomad-Ref server provides all-atom normal mode analyses for proteins with up to 2000 atoms. We have selected the protein, suggested in the TASK description 1BPT. We have calculated all-atom normal modes at a different temperatures (600K, 2000K). Furthermore we performed an elastic network calculation for this protein to compare it to the elastic network approximation.</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;"></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="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>{| border="1" style="text-align:center; border-spacing:0;"</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>{| border="1" style="text-align:center; border-spacing:0;"</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>|Temperature</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>|Temperature</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 </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 <ins class="diffchange diffchange-inline">7</ins></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;"><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>
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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>|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>
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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>
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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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<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;"></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;"></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 results of the all-atom calculation look very similar. As expected the modes, which were calculated at higher temperature show bigger movements compared to the lower temeperature. <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>We tried to compute the modes for the elastic network several times, but we got always the same spurious results, shown in the table above. Somehow, in all modes big unrealistic movements appear. We have removed all solvent atoms using repairPDB, so there should not be any molecules in the pdb causing these effects, so we do not have an explanation, what could have caused this effect. Especially as the all-atom calculations look very nice.</div></td>
</tr>
</table>Zacherhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_of_ARSA&diff=10994&oldid=prevZacher: /* NMA of ARSA */2011-08-12T14:28:56Z<p><span dir="auto"><span class="autocomment">NMA of ARSA</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 14:28, 12 August 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>|[[Image:nomaddist_arsa5.png|200px]]</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>|[[Image:nomaddist_arsa5.png|200px]]</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>
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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>
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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;"></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: #a3d3ff; 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;"></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>Mode 7 shows spurious results. In this mode two residues exhibit very large, completely unrealistic movements. We do not have an explanation for this, espaccially as we removed all atoms outside of the protein (water, metal ions, etc.). We also observed this, when we applied the method to 1BPT in the next section, where we als oremoved all additional moleculues. <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 shows spurious results. In this mode two residues exhibit very large, completely unrealistic movements. We do not have an explanation for this, espaccially as we removed all atoms outside of the protein (water, metal ions, etc.). We also observed this, when we applied the method to 1BPT in the next section, where we als oremoved all additional moleculues. <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>Modes 8-11, however, nicely agree with previous results. We obeserve again the movement of the helix in all modes. Especially in mode 11, we can see again the open-close movement around the enzymatic cleft.</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 other modes look again similar to the other results, though we observe the largest movements in these computations.</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 other modes look again similar to the other results, though we observe the largest movements in these computations.</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>
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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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</table>Zacherhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_of_ARSA&diff=10992&oldid=prevZacher: /* NMA of ARSA */2011-08-12T14:26:40Z<p><span dir="auto"><span class="autocomment">NMA of ARSA</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 14:26, 12 August 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="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>=== NMA of ARSA ===</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>=== NMA of ARSA ===</div></td>
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<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;"></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: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>We generated animated gifs from the pdb files for the first non-zero modes. These are - together with the distance of the movements - shown in the following tables:</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>
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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="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;"></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>|[[Image:nomaddist_arsa5.png|200px]]</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>|[[Image:nomaddist_arsa5.png|200px]]</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>
</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;"></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 shows spurious results. In this mode two residues exhibit very large, completely unrealistic movements. We do not have an explanation for this, espaccially as we removed all atoms outside of the protein (water, metal ions, etc.). We also observed this, when we applied the method to 1BPT in the next section, where we als oremoved all additional moleculues. <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>The other modes look again similar to the other results, though we observe the largest movements in these computations.</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>
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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>=== NMA of 1BPT ===</div></td>
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</table>Zacherhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_of_ARSA&diff=10988&oldid=prevZacher: /* oGNM – Gaussian network model */2011-08-12T14:22:09Z<p><span dir="auto"><span class="autocomment">oGNM – Gaussian network model</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 14:22, 12 August 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>The results nicely agree with the previous analyses. Again the terminal helix seems to be involved in the major movements within the protein (mode 7,8,11). Mode 9 and 10 show some mobibility also in the middle of the protein, but these movements are not as large as the movements of the terminal helix. This can be seen in the plot where all fluctuations are visualised together. <del class="diffchange diffchange-inline">One</del> <del class="diffchange diffchange-inline">can</del> <del class="diffchange diffchange-inline">clearly</del> <del class="diffchange diffchange-inline">see, that</del> mode <del class="diffchange diffchange-inline">7,</del> <del class="diffchange diffchange-inline">8</del> <del class="diffchange diffchange-inline">and</del> <del class="diffchange diffchange-inline">11</del> <del class="diffchange diffchange-inline">are</del> <del class="diffchange diffchange-inline">show</del> <del class="diffchange diffchange-inline">much</del> <del class="diffchange diffchange-inline">larger</del> <del class="diffchange diffchange-inline">movements</del> <del class="diffchange diffchange-inline">than</del> <del class="diffchange diffchange-inline">mode</del> <del class="diffchange diffchange-inline">9</del> <del class="diffchange diffchange-inline">and</del> <del class="diffchange diffchange-inline">10</del>. The movements of mode 9 and 10<del class="diffchange diffchange-inline">,</del> <del class="diffchange diffchange-inline">however,</del> <del class="diffchange diffchange-inline">should</del> be similar to mode 11 of WEBnma@ where we have also a mobility covering the whole protein and like here this mobility is much lower than the mobility of the helix.<del class="diffchange diffchange-inline"> Unfortunately we cannot visualize the movements itself from the output of oGNM, but at least, the mobility profiles to mode 11 of WEBnm@ look very similar. <br></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>The results nicely agree with the previous analyses. Again the terminal helix seems to be involved in the major movements within the protein (mode 7,8,11). Mode 9 and 10 show some mobibility also in the middle of the protein, but these movements are not as large as the movements of the terminal helix. This can be seen in the plot where all fluctuations are visualised together. <ins class="diffchange diffchange-inline">Mode</ins> <ins class="diffchange diffchange-inline">9</ins> <ins class="diffchange diffchange-inline">corresponds</ins> <ins class="diffchange diffchange-inline">to</ins> mode <ins class="diffchange diffchange-inline">5</ins> <ins class="diffchange diffchange-inline">from</ins> <ins class="diffchange diffchange-inline">the</ins> <ins class="diffchange diffchange-inline">ANM</ins> <ins class="diffchange diffchange-inline">webserver,</ins> <ins class="diffchange diffchange-inline">where</ins> <ins class="diffchange diffchange-inline">the</ins> <ins class="diffchange diffchange-inline">loops</ins> <ins class="diffchange diffchange-inline">close</ins> <ins class="diffchange diffchange-inline">the</ins> <ins class="diffchange diffchange-inline">enzymatic</ins> <ins class="diffchange diffchange-inline">cleft</ins> <ins class="diffchange diffchange-inline">(see previous</ins> <ins class="diffchange diffchange-inline">section)</ins>. The movements of mode 9 and 10 <ins class="diffchange diffchange-inline">might</ins> <ins class="diffchange diffchange-inline">also</ins> be similar to mode 11 of WEBnma@ where we have also a mobility covering the whole protein and like here this mobility is much lower than the mobility of the helix.</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>Furthermore, one can clearly see, that mode 7, 8 and 11 show much larger movements than mode 9 and 10. Unfortunately we cannot visualize the movements itself from the output of oGNM, but at least, the mobility profiles to mode 11 of WEBnm@ look very similar. <br></div></td>
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</table>Zacher