https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Simulations_Analysis_Hemochromatosis&feed=atom&action=historyMolecular Dynamics Simulations Analysis Hemochromatosis - Revision history2024-03-29T14:14:22ZRevision history for this page on the wikiMediaWiki 1.31.16https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Simulations_Analysis_Hemochromatosis&diff=28603&oldid=prevJoerdensv: /* Pymol analysis of average and bfactor */2012-08-31T20:26:29Z<p><span dir="auto"><span class="autocomment">Pymol analysis of average and bfactor</span></span></p>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>As one can see (compare: <xr id="tab:avg_bfactor"/>) there is a big change of b-factors when comparing the wildtype and both mutations we calculated. From both mutations the R224W one shows a bigger difference to the wildtype. As expected the positions "at the edges" <!-- most exposed TODO?--> and those not in a secondary structure tend to have higher fluctuations/higher b-factors. It is worth noting, that even the beta sheets on the right side of the R224W picture (position 180 and higher) have (compared to wildtype and C282S mutation) pretty high b-factors. Also one can see that a little helix is inserted into the average structure of the R224W average model (right part of the picture, high b-factor [red], position ~220-225).</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>As one can see (compare: <xr id="tab:avg_bfactor"/>) there is a big change of b-factors when comparing the wildtype and both mutations we calculated. From both mutations the R224W one shows a bigger difference to the wildtype. As expected the positions "at the edges" <!-- most exposed TODO?--> and those not in a secondary structure tend to have higher fluctuations/higher b-factors. It is worth noting, that even the beta sheets on the right side of the R224W picture (position 180 and higher) have (compared to wildtype and C282S mutation) pretty high b-factors. Also one can see that a little helix is inserted into the average structure of the R224W average model (right part of the picture, high b-factor [red], position ~220-225).</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="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>Also worth noting is, that the calculation of b-factors through NMA resulted in ones (cf. <xr id="tab:avg_bfactor"/> and [[Normal_Mode_Analysis_Hemochromatosis#Atomic_fluctuations| WebNMA fluctuations]]) similar to our MD calculated wildtype b-factors. It might also be possible that Elnemo (cf. [[Normal_Mode_Analysis_Hemochromatosis#B-factors| elNemo b-factors]]) has also calculated b-factors similar to the MD ones but are hidden in this depiction by our threshold.</div></td>
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</table>Joerdensvhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Simulations_Analysis_Hemochromatosis&diff=28599&oldid=prevBernhoferm: /* Conclusion */2012-08-31T20:12:21Z<p><span dir="auto"><span class="autocomment">Conclusion</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;"></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>When comparing the mutants' simulations to the wildtype, R224W seems to show a bit more differences than C282S. Especially the whole protein's flexibility seems to be increased, but if this is a blessing or a curse is yet unkown. C282S would seem to be the less harmful mutation of the two based on the MD results, yet it is known to be one of the more malicious ones.</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 comparing the mutants' simulations to the wildtype, R224W seems to show a bit more differences than C282S. Especially the whole protein's flexibility seems to be increased, but if this is a blessing or a curse is yet unkown. C282S would seem to be the less harmful mutation of the two based on the MD results, yet it is known to be one of the more malicious ones<ins class="diffchange diffchange-inline">. Overall we have gained some insight into the behavior of the three variants during the MD simulations, though it was sometimes hard to make sense of the information or to decide if it might be good or bad for the protein's function</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;"></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>This task showed the power of molecular dynamics simulations, but it also showed its weakness. While it provides a lot of data one could easily be deluded by the results of a single run (as the differences between our two runs showed). In order to get reliable result multiple simulations (5+) should be performed to get some kind of average or consensus and to eliminate outliers.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>This task showed the power of molecular dynamics simulations, but it also showed its weakness. While it provides a lot of data one could easily be deluded by the results of a single run (as the differences between our two runs showed). In order to get reliable result multiple simulations (5+) should be performed to get some kind of average or consensus and to eliminate outliers.</div></td>
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</table>Bernhofermhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Simulations_Analysis_Hemochromatosis&diff=28578&oldid=prevJoerdensv: /* Protein-Water */2012-08-31T19:57:02Z<p><span dir="auto"><span class="autocomment">Protein-Water</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:57, 31 August 2012</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>Although the inner-protein bonds seem to stay the same (compare section [[Molecular_Dynamics_Simulations_Analysis_Hemochromatosis#Protein-Protein|Protein-Protein]]), the bonds formed with hydrogen show a different behavior (see <xr id="tab:hbonds_pw"/>).</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>Although the inner-protein bonds seem to stay the same (compare section [[Molecular_Dynamics_Simulations_Analysis_Hemochromatosis#Protein-Protein|Protein-Protein]]), the bonds formed with hydrogen show a different behavior (see <xr id="tab:hbonds_pw"/>).</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="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>In case of the wildtype, both the number of hydrogen bonds as well as the number of pairs within 0.35nm are (compared to the values of the following timesteps) <del class="diffchange diffchange-inline">fairly low</del> at first, rising in the first ~600ps. This may be an indication that at first a dense protein state is existent. Also from ~8000-8600ps there is a drop in the number of hydrogen bonds, whereas the number of pairs within 0.35nm does not show an equal behavior. Overall the numbers tend to be at the same level each after the first 600ps rise.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>In case of the wildtype, both the number of hydrogen bonds as well as the number of pairs within 0.35nm are (compared to the values of the following timesteps) <ins class="diffchange diffchange-inline">lower</ins> at first, rising in the first ~600ps. This may be an indication that at first a dense protein state is existent. Also from ~8000-8600ps there is a drop in the number of hydrogen bonds, whereas the number of pairs within 0.35nm does not show an equal behavior. Overall the numbers tend to be at the same level each after the first 600ps rise.</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>
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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>The R224W model shows a different behavior over time:</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 R224W model shows a different behavior over time:</div></td>
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</table>Joerdensvhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Simulations_Analysis_Hemochromatosis&diff=28577&oldid=prevJoerdensv: /* Protein-Water */2012-08-31T19:56:01Z<p><span dir="auto"><span class="autocomment">Protein-Water</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:56, 31 August 2012</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>Although the inner-protein bonds seem to stay the same (compare section [[Molecular_Dynamics_Simulations_Analysis_Hemochromatosis#Protein-Protein|Protein-Protein]]), the bonds formed with hydrogen show a different behavior (see <xr id="tab:hbonds_pw"/>).</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>Although the inner-protein bonds seem to stay the same (compare section [[Molecular_Dynamics_Simulations_Analysis_Hemochromatosis#Protein-Protein|Protein-Protein]]), the bonds formed with hydrogen show a different behavior (see <xr id="tab:hbonds_pw"/>).</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>
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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>In case of the wildtype, both the number of hydrogen bonds as well as the number of pairs within 0.35nm are (compared to the <del class="diffchange diffchange-inline">rest</del>) fairly low at first, rising in the first ~600ps. This may be an indication that at first a dense protein state is existent. Also from ~8000-8600ps there is a drop in the number of hydrogen bonds, whereas the number of pairs within 0.35nm does not show an equal behavior. Overall the numbers tend to be at the same level each after the first 600ps rise.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>In case of the wildtype, both the number of hydrogen bonds as well as the number of pairs within 0.35nm are (compared to the <ins class="diffchange diffchange-inline">values of the following timesteps</ins>) fairly low at first, rising in the first ~600ps. This may be an indication that at first a dense protein state is existent. Also from ~8000-8600ps there is a drop in the number of hydrogen bonds, whereas the number of pairs within 0.35nm does not show an equal behavior. Overall the numbers tend to be at the same level each after the first 600ps rise.</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>
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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>The R224W model shows a different behavior over time:</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 R224W model shows a different behavior over time:</div></td>
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</table>Joerdensvhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Simulations_Analysis_Hemochromatosis&diff=28572&oldid=prevJoerdensv: /* Molecular dynamics simulations for HFE */2012-08-31T19:50:59Z<p><span dir="auto"><span class="autocomment">Molecular dynamics simulations for HFE</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>== Molecular dynamics simulations for HFE ==</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>== Molecular dynamics simulations for HFE ==</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>Note: All pictures/graphs shown here are from the first run (in case of 1a6zC[wildtype]-pictures) or second run (in case of R224W- or C282S-mutation). The reason for this is described under <del class="diffchange diffchange-inline">LINKTOMINDISTTODO</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>Note: All pictures/graphs shown here are from the first run (in case of 1a6zC[wildtype]-pictures) or second run (in case of R224W- or C282S-mutation). The reason for this is described under <ins class="diffchange diffchange-inline">section [[Molecular_Dynamics_Simulations_Analysis_Hemochromatosis#Minimum_distance_between_periodic_boundary_cells| Minimum distance between periodic boundary cells]]</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;"></td>
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</table>Joerdensvhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Simulations_Analysis_Hemochromatosis&diff=28562&oldid=prevBernhoferm: /* Conclusion */2012-08-31T19:24:27Z<p><span dir="auto"><span class="autocomment">Conclusion</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="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 comparing the mutants' simulations to the wildtype, R224W seems to show a bit more differences than C282S. Especially the whole protein's flexibility seems to be increased, but if this is a blessing or a curse is yet unkown. C282S would seem to be the less <del class="diffchange diffchange-inline">harmfull</del> mutation of the two based on the MD results, yet it is known to be one of the more malicious ones.</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 comparing the mutants' simulations to the wildtype, R224W seems to show a bit more differences than C282S. Especially the whole protein's flexibility seems to be increased, but if this is a blessing or a curse is yet unkown. C282S would seem to be the less <ins class="diffchange diffchange-inline">harmful</ins> mutation of the two based on the MD results, yet it is known to be one of the more malicious ones.</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 class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>This task showed the power of molecular dynamics simulations, but it also showed its weakness. While it provides a lot of data one could easily be deluded by the results of a single run (as the differences between our two runs showed). In order to get reliable result multiple simulations (5+) should be performed to get some kind of average or consensus and to eliminate outliers.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>This task showed the power of molecular dynamics simulations, but it also showed its weakness. While it provides a lot of data one could easily be deluded by the results of a single run (as the differences between our two runs showed). In order to get reliable result multiple simulations (5+) should be performed to get some kind of average or consensus and to eliminate outliers.</div></td>
</tr>
</table>Bernhofermhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Simulations_Analysis_Hemochromatosis&diff=28561&oldid=prevBernhoferm: /* Short task description */2012-08-31T19:23:14Z<p><span dir="auto"><span class="autocomment">Short task description</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>Detailed description: [[Task_10_-_Molecular_Dynamics_Simulations|Molecular dynamics simulations analysis]]</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>Detailed description: [[Task_10_-_Molecular_Dynamics_Simulations|Molecular dynamics simulations analysis]]</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: #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>Continuation of [[Molecular_Dynamics_Simulations_Hemochromatosis|task 8]]. Analysis of the MD simulations for the wildtype and two mutants (R224W and C282S).</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;"><div><br style="clear:both;"></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 style="clear:both;"></div></td>
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</table>Bernhofermhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Simulations_Analysis_Hemochromatosis&diff=28559&oldid=prevJoerdensv: /* Protein-Water */2012-08-31T19:21:11Z<p><span dir="auto"><span class="autocomment">Protein-Water</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:21, 31 August 2012</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 style="clear:both;"></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 style="clear:both;"></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>
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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>Although the inner-protein bonds seem to stay the same (compare section [[Molecular_Dynamics_Simulations_Analysis_Hemochromatosis#Protein-Protein|Protein-Protein]]), the bonds formed with hydrogen show a different behavior (<del class="diffchange diffchange-inline">compare</del> <xr id="tab:hbonds_pw"/>).</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>Although the inner-protein bonds seem to stay the same (compare section [[Molecular_Dynamics_Simulations_Analysis_Hemochromatosis#Protein-Protein|Protein-Protein]]), the bonds formed with hydrogen show a different behavior (<ins class="diffchange diffchange-inline">see</ins> <xr id="tab:hbonds_pw"/>).</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>
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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>In case of the wildtype, both the number of hydrogen bonds as well as the number of pairs within 0.35nm are (compared to the rest) fairly low at first, rising in the first ~600ps. This may be an indication that at first a dense protein state is existent. Also from ~8000-8600ps there is a drop in the number of hydrogen bonds, whereas the number of pairs within 0.35nm does not show an equal behavior. Overall the numbers tend to be at the same level each after the first 600ps rise.</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>In case of the wildtype, both the number of hydrogen bonds as well as the number of pairs within 0.35nm are (compared to the rest) fairly low at first, rising in the first ~600ps. This may be an indication that at first a dense protein state is existent. Also from ~8000-8600ps there is a drop in the number of hydrogen bonds, whereas the number of pairs within 0.35nm does not show an equal behavior. Overall the numbers tend to be at the same level each after the first 600ps rise.</div></td>
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</table>Joerdensvhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Simulations_Analysis_Hemochromatosis&diff=28558&oldid=prevJoerdensv: /* hydrogen-bonds between protein and protein / protein and water */2012-08-31T19:20:48Z<p><span dir="auto"><span class="autocomment">hydrogen-bonds between protein and protein / protein and water</span></span></p>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br style="clear:both;"></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="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">hydrogen</del>-bonds between protein and protein / protein and water ===</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>=== <ins class="diffchange diffchange-inline">Hydrogen</ins>-bonds between protein and protein / protein and water ===</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>==== Protein-Protein ====</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>==== Protein-Protein ====</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 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 style="clear:both;"></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>
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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 calculations show that in each of the three cases the number of bonds within the protein as well as their distances tend to stay the same.</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 calculations show that in each of the three cases<ins class="diffchange diffchange-inline"> (see <xr id="tab:hbonds_pp"/>)</ins> the number of bonds within the protein as well as their distances tend to stay the same.</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="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>Although the inner-protein bonds seem to stay the same (<del class="diffchange diffchange-inline">see</del> <del class="diffchange diffchange-inline">PREVIOUSSECTIONTODO</del>), the bonds formed with hydrogen show a different behavior.</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>Although the inner-protein bonds seem to stay the same (<ins class="diffchange diffchange-inline">compare</ins> <ins class="diffchange diffchange-inline">section [[Molecular_Dynamics_Simulations_Analysis_Hemochromatosis#Protein-Protein|Protein-Protein]]</ins>), the bonds formed with hydrogen show a different behavior<ins class="diffchange diffchange-inline"> (compare <xr id="tab:hbonds_pw"/>)</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;"></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In case of the wildtype, both the number of hydrogen bonds as well as the number of pairs within 0.35nm are (compared to the rest) fairly low at first, rising in the first ~600ps. This may be an indication that at first a dense protein state is existent. Also from ~8000-8600ps there is a drop in the number of hydrogen bonds, whereas the number of pairs within 0.35nm does not show an equal behavior. Overall the numbers tend to be at the same level each after the first 600ps rise.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In case of the wildtype, both the number of hydrogen bonds as well as the number of pairs within 0.35nm are (compared to the rest) fairly low at first, rising in the first ~600ps. This may be an indication that at first a dense protein state is existent. Also from ~8000-8600ps there is a drop in the number of hydrogen bonds, whereas the number of pairs within 0.35nm does not show an equal behavior. Overall the numbers tend to be at the same level each after the first 600ps rise.</div></td>
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</table>Joerdensvhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Simulations_Analysis_Hemochromatosis&diff=28555&oldid=prevJoerdensv: /* solvent accessible surface area */2012-08-31T19:15:16Z<p><span dir="auto"><span class="autocomment">solvent accessible surface area</span></span></p>
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