https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Canavan_Disease:_Task_05_-_Homology_Modelling&feed=atom&action=history
Canavan Disease: Task 05 - Homology Modelling - Revision history
2024-03-28T11:47:41Z
Revision history for this page on the wiki
MediaWiki 1.31.16
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Canavan_Disease:_Task_05_-_Homology_Modelling&diff=38740&oldid=prev
Boehma: /* Dataset */
2013-09-05T11:12:13Z
<p><span dir="auto"><span class="autocomment">Dataset</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 11:12, 5 September 2013</td>
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<td colspan="2" class="diff-lineno">Line 1:</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>'''Homology Modelling''' is a very important step: Since not always a structure to the protein of interest is known, models can help understanding the protein. Even SNPs in the sequence can make a difference in those models. Therefore such an investigation is indispensable.</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>'''Homology Modelling''' is a very important step: Since not always a structure to the protein of interest is known, models can help understanding the protein. Even SNPs in the sequence can make a difference in those models. Therefore such an investigation is indispensable.</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>== Dataset ==</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>== Dataset ==</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>The models are calculated with three different homology modelling tools: '''Modeller'''<del class="diffchange diffchange-inline"> (as explained in [https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Using_Modeller_for_TASK_4 description] of the Task)</del>, '''[http://swissmodel.expasy.org SwissModel]''' and '''[http://zhanglab.ccmb.med.umich.edu/I-TASSER/ iTasser]'''. To compare the modelling algorithms two sequences per sequence similarity set were chosen as template. For a description of the dataset see '''<xr id="dataset"></xr>'''.</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 models are calculated with three different homology modelling tools: '''Modeller''', '''[http://swissmodel.expasy.org SwissModel]''' and '''[http://zhanglab.ccmb.med.umich.edu/I-TASSER/ iTasser]'''. To compare the modelling algorithms two sequences per sequence similarity set were chosen as template. For a description of the dataset see '''<xr id="dataset"></xr>'''.</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><figtable id="dataset"></div></td>
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Boehma
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Canavan_Disease:_Task_05_-_Homology_Modelling&diff=38704&oldid=prev
Mahlich: /* SwissModel */
2013-09-05T10:24:58Z
<p><span dir="auto"><span class="autocomment">SwissModel</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 10:24, 5 September 2013</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;"><div>Regarding the models created from templates with a sequence similarity of less than 30% to 2O4H, the remark that SwissModel was not able to form a model with 1YW4 as template has to be made. The modelling process with 2QJ8 as template has been successful however. </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>Regarding the models created from templates with a sequence similarity of less than 30% to 2O4H, the remark that SwissModel was not able to form a model with 1YW4 as template has to be made. The modelling process with 2QJ8 as template has been successful however. </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>Taking a closer look at the model created from 2QJ8 is <del class="diffchange diffchange-inline">get</del> visible that SwissModel at least for this specific example does not perform as well as Modeller using a template with low sequence similarity. The overall positioning of the atoms is correct, but the prediction of secondary structure elements is much worse. Some residues do not even have a predicted spacial position (see '''<xr id="2QJ8_sm"></xr>''').</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>Taking a closer look at the model created from 2QJ8 is <ins class="diffchange diffchange-inline">gets</ins> visible that SwissModel at least for this specific example does not perform as well as Modeller using a template with low sequence similarity. The overall positioning of the atoms is correct, but the prediction of secondary structure elements is much worse. Some residues do not even have a predicted spacial position (see '''<xr id="2QJ8_sm"></xr>''').</div></td>
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Mahlich
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Canavan_Disease:_Task_05_-_Homology_Modelling&diff=38702&oldid=prev
Mahlich: /* SwissModel */
2013-09-05T10:24:03Z
<p><span dir="auto"><span class="autocomment">SwissModel</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 10:24, 5 September 2013</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>=== SwissModel ===</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>=== SwissModel ===</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>Examining the models created by SwissModel with high sequence similarity templates in Pymol together with the templates and target, reveals that SwissModel creates very accurate models as well. One visible difference compared the models created by Modeller is that SwissModel seems to created the model for the length of the target opposed to Modeller where for example the N and C-terminus of the polypeptide is well extended over the length of the actual target (see '''<xr id="2O53_sm"></xr>''' and '''<xr id="2GU2_sm"></xr>''').</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>Examining the models created by SwissModel with high sequence similarity templates in Pymol together with the templates and target, reveals that SwissModel creates very accurate models as well. One visible difference compared<ins class="diffchange diffchange-inline"> to</ins> the models created by Modeller is that SwissModel seems to created the model for the length of the target opposed to Modeller where for example the N and C-terminus of the polypeptide is well extended over the length of the actual target (see '''<xr id="2O53_sm"></xr>''' and '''<xr id="2GU2_sm"></xr>''').</div></td>
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Mahlich
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Canavan_Disease:_Task_05_-_Homology_Modelling&diff=38701&oldid=prev
Mahlich: /* Modeller with Single Sequence Template */
2013-09-05T10:20:59Z
<p><span dir="auto"><span class="autocomment">Modeller with Single Sequence Template</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 10:20, 5 September 2013</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>=== Modeller with Single Sequence Template===</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>=== Modeller with Single Sequence Template===</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 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>Modeller produced extremely accurate models for the target protein given templates with a high sequence similarity. Both 2O53 and 2GU2 are already highly similar in structure if visually compared to 2O4H. Performing a structural alignment of the template structures to 2O4H result in <del class="diffchange diffchange-inline">RMDS</del> below 1Å. Therefore it is to be expected that the models generated should be very accurate, and this is exactly what can be observed (see '''<xr id="2O53_md"></xr>''' and '''<xr id="2GU2_md"></xr>''').</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>Modeller produced extremely accurate models for the target protein given templates with a high sequence similarity. Both 2O53 and 2GU2 are already highly similar in structure if visually compared to 2O4H. Performing a structural alignment of the template structures to 2O4H result in <ins class="diffchange diffchange-inline">RMSDs</ins> below 1Å. Therefore it is to be expected that the models generated should be very accurate, and this is exactly what can be observed (see '''<xr id="2O53_md"></xr>''' and '''<xr id="2GU2_md"></xr>''').</div></td>
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Mahlich
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Canavan_Disease:_Task_05_-_Homology_Modelling&diff=38699&oldid=prev
Mahlich: /* Model creation */
2013-09-05T10:20:19Z
<p><span dir="auto"><span class="autocomment">Model creation</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 10:20, 5 September 2013</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>== Model creation ==</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>== Model creation ==</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 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>Each modelling algorithm was used to produce models for 2O4H (as representative for aspartoacylase) based on four different template proteins. Those models can be examined in the following section <del class="diffchange diffchange-inline">except</del> the model that SwissModel should have created based in 1YW4, as SwissModel was not able to perform this task.</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>Each modelling algorithm was used to produce models for 2O4H (as representative for aspartoacylase) based on four different template proteins. Those models can be examined in the following section<ins class="diffchange diffchange-inline">.</ins> <ins class="diffchange diffchange-inline">An exception is</ins> the model that SwissModel should have created based in 1YW4, as SwissModel was not able to perform this task.</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>=== Modeller with Single Sequence Template===</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>=== Modeller with Single Sequence Template===</div></td>
</tr>
</table>
Mahlich
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Canavan_Disease:_Task_05_-_Homology_Modelling&diff=38698&oldid=prev
Mahlich at 10:19, 5 September 2013
2013-09-05T10:19:10Z
<p></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 10:19, 5 September 2013</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</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>'''Homology Modelling''' is<del class="diffchange diffchange-inline"> also</del> a very important step: Since not always a structure to the protein of interest is known, models can help understanding the protein. Even SNPs in the sequence can make a difference in those models. <del class="diffchange diffchange-inline">Such</del> investigation is<del class="diffchange diffchange-inline"> therefore</del> indispensable.</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>'''Homology Modelling''' is a very important step: Since not always a structure to the protein of interest is known, models can help understanding the protein. Even SNPs in the sequence can make a difference in those models. <ins class="diffchange diffchange-inline">Therefore such an</ins> investigation is indispensable.</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>== Dataset ==</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>== Dataset ==</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 models are calculated with three different homology modelling tools: '''Modeller''' (as explained in [https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Using_Modeller_for_TASK_4 description] of the Task), '''[http://swissmodel.expasy.org SwissModel]''' and '''[http://zhanglab.ccmb.med.umich.edu/I-TASSER/ iTasser]'''. To compare the modelling algorithms two sequences per sequence similarity set were chosen as template. For a description of the dataset see '''<xr id="dataset"></xr>'''.</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 models are calculated with three different homology modelling tools: '''Modeller''' (as explained in [https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Using_Modeller_for_TASK_4 description] of the Task), '''[http://swissmodel.expasy.org SwissModel]''' and '''[http://zhanglab.ccmb.med.umich.edu/I-TASSER/ iTasser]'''. To compare the modelling algorithms two sequences per sequence similarity set were chosen as template. For a description of the dataset see '''<xr id="dataset"></xr>'''.</div></td>
</tr>
<!-- diff cache key wikidb:diff:wikidiff2:1.12:old-38692:rev-38698:1.7.3:0 -->
</table>
Mahlich
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Canavan_Disease:_Task_05_-_Homology_Modelling&diff=38692&oldid=prev
Boehma: /* Dataset */
2013-09-05T10:01:43Z
<p><span dir="auto"><span class="autocomment">Dataset</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 10:01, 5 September 2013</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 23:</td>
<td colspan="2" class="diff-lineno">Line 23:</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 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>
<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><center><small>'''<caption>''' Overview of the dataset composition for <del class="diffchange diffchange-inline">Task05</del>, containing a brief description of the the chosen structures<br>and the sequence identity to the reference ASPA protein.</caption></small></center></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><center><small>'''<caption>''' Overview of the dataset composition for <ins class="diffchange diffchange-inline">Task 05</ins>, containing a brief description of the the chosen structures<br>and the sequence identity to the reference ASPA protein.</caption></small></center></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></figtable></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></figtable></div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
</table>
Boehma
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Canavan_Disease:_Task_05_-_Homology_Modelling&diff=38691&oldid=prev
Boehma: /* Dataset */
2013-09-05T10:01:22Z
<p><span dir="auto"><span class="autocomment">Dataset</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 10:01, 5 September 2013</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</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>'''Homology Modelling''' is also a very important step: Since not always a structure to the protein of interest is known, models can help understanding the protein. Even SNPs in the sequence can make a difference in those models. Such investigation is therefore indispensable.</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>'''Homology Modelling''' is also a very important step: Since not always a structure to the protein of interest is known, models can help understanding the protein. Even SNPs in the sequence can make a difference in those models. Such investigation is therefore indispensable.</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>== Dataset ==</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>== Dataset ==</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 models are calculated with three different homology modelling tools: '''Modeller''' (as explained in [https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Using_Modeller_for_TASK_4 description] of the <del class="diffchange diffchange-inline">task</del>), '''[http://swissmodel.expasy.org SwissModel]''' and '''[http://zhanglab.ccmb.med.umich.edu/I-TASSER/ iTasser]'''. To compare the modelling algorithms two sequences per sequence similarity set were chosen as template. For a description of the dataset see '''<xr id="dataset"></xr>'''.</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 models are calculated with three different homology modelling tools: '''Modeller''' (as explained in [https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Using_Modeller_for_TASK_4 description] of the <ins class="diffchange diffchange-inline">Task</ins>), '''[http://swissmodel.expasy.org SwissModel]''' and '''[http://zhanglab.ccmb.med.umich.edu/I-TASSER/ iTasser]'''. To compare the modelling algorithms two sequences per sequence similarity set were chosen as template. For a description of the dataset see '''<xr id="dataset"></xr>'''.</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><figtable id="dataset"></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><figtable id="dataset"></div></td>
</tr>
</table>
Boehma
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Canavan_Disease:_Task_05_-_Homology_Modelling&diff=38581&oldid=prev
Mahlich: /* Dataset */
2013-09-04T18:10:18Z
<p><span dir="auto"><span class="autocomment">Dataset</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 18:10, 4 September 2013</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</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>'''Homology Modelling''' is also a very important step: Since not always a structure to the protein of interest is known, models can help understanding the protein. Even SNPs in the sequence can make a difference in those models. Such investigation is therefore indispensable.</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>'''Homology Modelling''' is also a very important step: Since not always a structure to the protein of interest is known, models can help understanding the protein. Even SNPs in the sequence can make a difference in those models. Such investigation is therefore indispensable.</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>== Dataset ==</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>== Dataset ==</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 models are calculated with three different homology modelling tools: Modeller (as explained in [https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Using_Modeller_for_TASK_4 description] of the task), [http://swissmodel.expasy.org SwissModel] and [http://zhanglab.ccmb.med.umich.edu/I-TASSER/ iTasser]. To compare the modelling algorithms two sequences per sequence similarity set were chosen as template. For a description of the dataset see '''<xr id="dataset"></xr>'''.</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 models are calculated with three different homology modelling tools: <ins class="diffchange diffchange-inline">'''</ins>Modeller<ins class="diffchange diffchange-inline">'''</ins> (as explained in [https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Using_Modeller_for_TASK_4 description] of the task), <ins class="diffchange diffchange-inline">'''</ins>[http://swissmodel.expasy.org SwissModel]<ins class="diffchange diffchange-inline">'''</ins> and <ins class="diffchange diffchange-inline">'''</ins>[http://zhanglab.ccmb.med.umich.edu/I-TASSER/ iTasser]<ins class="diffchange diffchange-inline">'''</ins>. To compare the modelling algorithms two sequences per sequence similarity set were chosen as template. For a description of the dataset see '''<xr id="dataset"></xr>'''.</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><figtable id="dataset"></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><figtable id="dataset"></div></td>
</tr>
</table>
Mahlich
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Canavan_Disease:_Task_05_-_Homology_Modelling&diff=38563&oldid=prev
Mahlich: /* Dataset */
2013-09-04T17:55:20Z
<p><span dir="auto"><span class="autocomment">Dataset</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 17:55, 4 September 2013</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</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>'''Homology Modelling''' is also a very important step: Since not always a structure to the protein of interest is known, models can help understanding the protein. Even SNPs in the sequence can make a difference in those models. Such investigation is therefore indispensable.</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>'''Homology Modelling''' is also a very important step: Since not always a structure to the protein of interest is known, models can help understanding the protein. Even SNPs in the sequence can make a difference in those models. Such investigation is therefore indispensable.</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>== Dataset ==</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>== Dataset ==</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 models are calculated with three different homology modelling tools: Modeller (as explained in [https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Using_Modeller_for_TASK_4 description] of the task), [http://swissmodel.expasy.org SwissModel] and [http://zhanglab.ccmb.med.umich.edu/I-TASSER/ iTasser]. To compare the modelling algorithms two sequences per sequence similarity set were chosen as template<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>The models are calculated with three different homology modelling tools: Modeller (as explained in [https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Using_Modeller_for_TASK_4 description] of the task), [http://swissmodel.expasy.org SwissModel] and [http://zhanglab.ccmb.med.umich.edu/I-TASSER/ iTasser]. To compare the modelling algorithms two sequences per sequence similarity set were chosen as template<ins class="diffchange diffchange-inline">.</ins> <ins class="diffchange diffchange-inline">For a description of the dataset see '''<xr id="dataset"></xr>'''.</ins></div></td>
</tr>
<tr>
<td class="diff-marker"> </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><figtable id="dataset"></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><figtable id="dataset"></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="background-color: #f8f9fa; color: #222; font-size: 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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><center><small>'''<caption>''' Overview of the dataset composition for <del class="diffchange diffchange-inline">Task 05</del>, containing a brief description of the the chosen structures<br>and the sequence identity to the reference ASPA protein.</caption></small></center></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><center><small>'''<caption>''' Overview of the dataset composition for <ins class="diffchange diffchange-inline">Task05</ins>, containing a brief description of the the chosen structures<br>and the sequence identity to the reference ASPA protein.</caption></small></center></div></td>
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Mahlich