https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Gaucher_Disease:_Task_09_-_Structure-based_mutation_analysis&feed=atom&action=history
Gaucher Disease: Task 09 - Structure-based mutation analysis - Revision history
2024-03-29T10:26:02Z
Revision history for this page on the wiki
MediaWiki 1.31.16
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Gaucher_Disease:_Task_09_-_Structure-based_mutation_analysis&diff=38953&oldid=prev
Kalemanovm: /* 2. Visualization of the mutations to work with */
2013-09-29T23:52:40Z
<p><span dir="auto"><span class="autocomment">2. Visualization of the mutations to work with</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 23:52, 29 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;"><div><figtable id="mutations"></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>{|class="colBasic2"</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>{|class="colBasic2"</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>! Reference || Codon <del class="diffchange diffchange-inline">Number</del> (UniProt) || Codon <del class="diffchange diffchange-inline">Number</del> (PDB) || Codon change || Amino <del class="diffchange diffchange-inline">Acid</del> change || Polarity || Charge (pH) || Disease causing?</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>! Reference || Codon <ins class="diffchange diffchange-inline">number</ins> (UniProt) || Codon <ins class="diffchange diffchange-inline">number</ins> (PDB) || Codon change || Amino <ins class="diffchange diffchange-inline">acid</ins> change || Polarity || Charge (pH) || Disease causing?</div></td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td 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>| [http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=368786234 rs368786234]|| 77 || 38 || AG<span style="color:#FF0040">'''C'''</span> ⇒ AG<span style="color:#FF0040">'''A'''</span> || Ser ⇒ Arg (S77R) ||polar ⇒ polar || neutral ⇒ positive || FALSE</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>| [http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=368786234 rs368786234]|| 77 || 38 || AG<span style="color:#FF0040">'''C'''</span> ⇒ AG<span style="color:#FF0040">'''A'''</span> || Ser ⇒ Arg (S77R) ||polar ⇒ polar || neutral ⇒ positive || FALSE</div></td>
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Kalemanovm
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Gaucher_Disease:_Task_09_-_Structure-based_mutation_analysis&diff=38952&oldid=prev
Kalemanovm: /* 2. Visualization of the mutations to work with */
2013-09-29T22:40:54Z
<p><span dir="auto"><span class="autocomment">2. Visualization of the mutations to work with</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 22:40, 29 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><figtable id="mutations"></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>{|class="colBasic2"</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>{|class="colBasic2"</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>! Reference<del class="diffchange diffchange-inline"> || Codon change</del> || Codon Number (UniProt) || Codon Number (PDB) || Amino Acid change || Polarity || Charge (pH) || Disease causing?</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>! Reference || Codon Number (UniProt) || Codon Number (PDB)<ins class="diffchange diffchange-inline"> || Codon change</ins> || Amino Acid change || Polarity || Charge (pH) || Disease causing?</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>|-</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td 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>| [http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=368786234 rs368786234]|| AG<span style="color:#FF0040">'''C'''</span> ⇒ AG<span style="color:#FF0040">'''A'''</span><del class="diffchange diffchange-inline"> || 77 || 38</del> || Ser ⇒ Arg (S77R) ||polar ⇒ polar || neutral ⇒ positive || FALSE</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>| [http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=368786234 rs368786234]<ins class="diffchange diffchange-inline">|| 77 || 38 </ins>|| AG<span style="color:#FF0040">'''C'''</span> ⇒ AG<span style="color:#FF0040">'''A'''</span> || Ser ⇒ Arg (S77R) ||polar ⇒ polar || neutral ⇒ positive || FALSE</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td 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>| [http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=374003673 rs374003673]|| A<span style="color:#FF0040">'''A'''</span>T ⇒ A<span style="color:#FF0040">'''G'''</span>T<del class="diffchange diffchange-inline"> || 141 || 102</del> || Asn ⇒ Ser (N141S) || polar ⇒ polar || neutral ⇒ neutral || FALSE </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>| [http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=374003673 rs374003673]<ins class="diffchange diffchange-inline">|| 141 || 102 </ins>|| A<span style="color:#FF0040">'''A'''</span>T ⇒ A<span style="color:#FF0040">'''G'''</span>T || Asn ⇒ Ser (N141S) || polar ⇒ polar || neutral ⇒ neutral || FALSE </div></td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td 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>| CM992894|| G<span style="color:#FF0040">'''G'''</span>A ⇒ G<span style="color:#FF0040">'''A'''</span>A<del class="diffchange diffchange-inline">|| 241 || 202 </del>|| Gly ⇒ Glu (G241E) || nonpolar ⇒ polar || neutral ⇒ negative || TRUE</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>| CM992894<ins class="diffchange diffchange-inline">|| 241 || 202 </ins>|| G<span style="color:#FF0040">'''G'''</span>A ⇒ G<span style="color:#FF0040">'''A'''</span>A|| Gly ⇒ Glu (G241E) || nonpolar ⇒ polar || neutral ⇒ negative || TRUE</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>
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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>| CM880036|| A<span style="color:#FF0040">'''A'''</span>C ⇒ A<span style="color:#FF0040">'''G'''</span>C<del class="diffchange diffchange-inline"> || 409 || 370</del> || Asn ⇒ Ser (N409S) || polar ⇒ polar || neutral ⇒ neutral || TRUE </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>| CM880036<ins class="diffchange diffchange-inline">|| 409 || 370 </ins>|| A<span style="color:#FF0040">'''A'''</span>C ⇒ A<span style="color:#FF0040">'''G'''</span>C || Asn ⇒ Ser (N409S) || polar ⇒ polar || neutral ⇒ neutral || TRUE </div></td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|- </div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|- </div></td>
</tr>
<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>| CM870010|| C<span style="color:#FF0040">'''T'''</span>G ⇒ C<span style="color:#FF0040">'''C'''</span>G<del class="diffchange diffchange-inline"> || 483 || 444</del> || Leu ⇒ Pro (L483P) || nonpolar ⇒ nonpolar || neutral ⇒ neutral || TRUE</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>| CM870010<ins class="diffchange diffchange-inline">|| 483 || 444 </ins>|| C<span style="color:#FF0040">'''T'''</span>G ⇒ C<span style="color:#FF0040">'''C'''</span>G || Leu ⇒ Pro (L483P) || nonpolar ⇒ nonpolar || neutral ⇒ neutral || TRUE</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>|}</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|}</div></td>
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<td 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><center><small>'''<caption>''' Selected mutations of GBA sequence P04062. Mapping of the UniProt positions onto the PDB ATOM sequence is given. </caption></small></center></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><center><small>'''<caption>''' Selected mutations of GBA sequence P04062. Mapping of the UniProt positions onto the PDB ATOM sequence is given. </caption></small></center></div></td>
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Kalemanovm
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Gaucher_Disease:_Task_09_-_Structure-based_mutation_analysis&diff=38931&oldid=prev
Kalemanovm: /* foldX */
2013-09-28T17:23:28Z
<p><span dir="auto"><span class="autocomment">foldX</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 17:23, 28 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>File:2V3E_B_mutant_38R.png| Mutation S77R. There is almost no difference in the conformation. However, foldX predicts two additional hydrogen bonds between the Argenine side chain: one to a residues in a proximate loop and the second is a big Tyrosine side chain from the same beta strand.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>File:2V3E_B_mutant_38R.png| Mutation S77R. There is almost no difference in the conformation. However, foldX predicts two additional hydrogen bonds between the Argenine side chain: one to a residues in a proximate loop and the second is a big Tyrosine side chain from the same beta strand.</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>File:2V3E_B_mutant_102S.png| Mutation N141S. There is almost no difference in the conformation and the same hydrogen bonds are predicted.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>File:2V3E_B_mutant_102S.png| Mutation N141S. There is almost no difference in the conformation and the same hydrogen bonds are predicted.</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>File:2V3E_B_mutant_202E.png| Mutation G241E. In foldX the conformation of the Glutamate side chain is a little bit different, but it has no meaning, as it lies on the outside of the protein. Also the binding partner side chain has a little bit different angle, so that two hydrogen bonds, instead<del class="diffchange diffchange-inline"> of</del> of only one in SCWRL, are formed.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>File:2V3E_B_mutant_202E.png| Mutation G241E. In foldX the conformation of the Glutamate side chain is a little bit different, but it has no meaning, as it lies on the outside of the protein. Also the binding partner side chain has a little bit different angle, so that two hydrogen bonds, instead of only one in SCWRL, are formed.</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>File:2V3E_B_mutant_370S.png| Mutation N409S. SCWRL and foldX agree in the conformation of the mutated and the binding residues, including the hydrogen bonds formed between them, apart from tiny shifts.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>File:2V3E_B_mutant_370S.png| Mutation N409S. SCWRL and foldX agree in the conformation of the mutated and the binding residues, including the hydrogen bonds formed between them, apart from tiny shifts.</div></td>
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<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>File:2V3E_B_mutant_444P.png| Mutation L483P. Also here SCWRL and foldX predict nearly the same conformation of the Proline (and the residue which forms a hydrogen bond in WT with the Leucine).</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>File:2V3E_B_mutant_444P.png| Mutation L483P. Also here SCWRL and foldX predict nearly the same conformation of the Proline (and the residue which forms a hydrogen bond in WT with the Leucine).</div></td>
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Kalemanovm
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Gaucher_Disease:_Task_09_-_Structure-based_mutation_analysis&diff=38929&oldid=prev
Kalemanovm: /* 1. Choice of a structure to work with */
2013-09-27T19:03:56Z
<p><span dir="auto"><span class="autocomment">1. Choice of a structure to work with</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>|[http://www.pdb.org/pdb/files/2V3E.pdb 2V3E] || 2.0 || A/B || 40-536 (92.7%) || A: 31, (498-503), B: (-1), (498-503) || A: -1-30, 32-497, B: '''0-497''' || 0.163 || 0.220 || '''7.5''' || 100</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>|[http://www.pdb.org/pdb/files/2V3E.pdb 2V3E] || 2.0 || A/B || 40-536 (92.7%) || A: 31, (498-503), B: (-1), (498-503) || A: -1-30, 32-497, B: '''0-497''' || 0.163 || 0.220 || '''7.5''' || 100</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>''' 2V3E, chain B, the chosen reference structure of GBA sequence P04062.</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>'''<ins class="diffchange diffchange-inline"> Properties of</ins> 2V3E, chain B, the chosen reference structure of GBA sequence P04062.</caption></small></center></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></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></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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Kalemanovm
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Gaucher_Disease:_Task_09_-_Structure-based_mutation_analysis&diff=38798&oldid=prev
Kalemanovm: /* Minimise */
2013-09-05T17:50:32Z
<p><span dir="auto"><span class="autocomment">Minimise</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 17:50, 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;"><div></figure></div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></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>To conclude, SQWRL and foldX are both pretty good tools for calculating the energy difference and the structural change of a protein after a point mutation. There is almost no difference <del class="diffchange diffchange-inline">between</del> the resulting structures, in particular the conformations of the mutated residues and their <del class="diffchange diffchange-inline">environment,</del> <del class="diffchange diffchange-inline">between</del> <del class="diffchange diffchange-inline">the</del> <del class="diffchange diffchange-inline">two programs</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>To conclude, SQWRL and foldX are both pretty good tools for calculating the energy difference and the structural change of a protein after a point mutation. There is almost no difference <ins class="diffchange diffchange-inline">in</ins> the resulting structures<ins class="diffchange diffchange-inline"> between the two programs</ins>, in particular the<ins class="diffchange diffchange-inline"> predicted</ins> conformations of the mutated residues and their <ins class="diffchange diffchange-inline">environments</ins> <ins class="diffchange diffchange-inline">are</ins> <ins class="diffchange diffchange-inline">very</ins> <ins class="diffchange diffchange-inline">similar</ins>.</div></td>
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Kalemanovm
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Gaucher_Disease:_Task_09_-_Structure-based_mutation_analysis&diff=38797&oldid=prev
Kalemanovm: /* Minimise */
2013-09-05T17:49:01Z
<p><span dir="auto"><span class="autocomment">Minimise</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 17:49, 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><gallery widths=300px heights=200px perrow="3"></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><gallery widths=300px heights=200px perrow="3"></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>File:2V3E_B_S38R_minimised-scwrl_vs_foldx.png| Mutation S77R.<del class="diffchange diffchange-inline"> There is almost no difference in the conformation for this and also the following mutations. </del></div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>File:2V3E_B_S38R_minimised-scwrl_vs_foldx.png| Mutation S77R.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>File:2V3E_B_N102S_minimised-scwrl_vs_foldx.png| Mutation N141S.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>File:2V3E_B_N102S_minimised-scwrl_vs_foldx.png| Mutation N141S.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>File:2V3E_B_G202E_minimised-scwrl_vs_foldx.png| Mutation G241E.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>File:2V3E_B_G202E_minimised-scwrl_vs_foldx.png| Mutation G241E.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>File:2V3E_B_L444P_minimised-scwrl_vs_foldx.png| Mutation L483P.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>File:2V3E_B_L444P_minimised-scwrl_vs_foldx.png| Mutation L483P.</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></gallery></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></gallery></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><small>'''<caption>''' Comparison between the mutants created with SCWRL after two minimise iterations (gray protein, orange mutated residue) and foldX after one minimise iteration (lime protein, cyan mutated residue).</caption></small></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><small>'''<caption>''' Comparison between the mutants created with SCWRL after two minimise iterations (gray protein, orange mutated residue) and foldX after one minimise iteration (lime protein, cyan mutated residue).<ins class="diffchange diffchange-inline"> There is almost no difference in the conformations of all the mutations. </ins></caption></small></div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></figure></div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
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Kalemanovm
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Gaucher_Disease:_Task_09_-_Structure-based_mutation_analysis&diff=38796&oldid=prev
Kalemanovm: /* Minimise */
2013-09-05T17:47:45Z
<p><span dir="auto"><span class="autocomment">Minimise</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 17:47, 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>File:2V3E_B_L444P_minimised-scwrl_vs_foldx.png| Mutation L483P.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>File:2V3E_B_L444P_minimised-scwrl_vs_foldx.png| Mutation L483P.</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></gallery></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></gallery></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><small>'''<caption>''' Comparison between the mutants created with SCWRL after two minimise iterations (gray protein, orange mutated residue<del class="diffchange diffchange-inline">, yellow polar contacts</del>) and foldX after one minimise iteration (lime protein, cyan mutated residue<del class="diffchange diffchange-inline">, dark cyan polar contacts</del>).</caption></small></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><small>'''<caption>''' Comparison between the mutants created with SCWRL after two minimise iterations (gray protein, orange mutated residue) and foldX after one minimise iteration (lime protein, cyan mutated residue).</caption></small></div></td>
</tr>
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<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></figure></div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></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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Kalemanovm
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Gaucher_Disease:_Task_09_-_Structure-based_mutation_analysis&diff=38795&oldid=prev
Kalemanovm: /* Minimise */
2013-09-05T17:46:58Z
<p><span dir="auto"><span class="autocomment">Minimise</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 17:46, 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>Another interesting observation is that after reaching the lowest energy in the second minimise iterations in the WT and the foldX mutants, the energy rises constantly in the consequent runs. This probably means that the minimal local energy is reached in the second iteration and then the computation of the gradient at the minimal point can only lead to a higher energy value, maybe to another local minimum with a higher energy. A different pattern happens during the minimisation of the SCWRL mutants: after reaching the local minimal energy already after the first iteration, in the second iteration the energy rises, however it falls a little again in the third iteration, thought not into the same local minimum as in the first iteration. This indicates that a second "suboptimal" local minimum is found. After the forth iteration the energy rises again. </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>Another interesting observation is that after reaching the lowest energy in the second minimise iterations in the WT and the foldX mutants, the energy rises constantly in the consequent runs. This probably means that the minimal local energy is reached in the second iteration and then the computation of the gradient at the minimal point can only lead to a higher energy value, maybe to another local minimum with a higher energy. A different pattern happens during the minimisation of the SCWRL mutants: after reaching the local minimal energy already after the first iteration, in the second iteration the energy rises, however it falls a little again in the third iteration, thought not into the same local minimum as in the first iteration. This indicates that a second "suboptimal" local minimum is found. After the forth iteration the energy rises again. </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="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>We compared the mutant structures in Pymol again after the minimise runs reaching the best energies: after the second round for SQWRL and the first round for foldX (<<del class="diffchange diffchange-inline">rx</del> id="minimise"/>).</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>We compared the mutant structures in Pymol again after the minimise runs reaching the best energies: after the second round for SQWRL and the first round for foldX (<<ins class="diffchange diffchange-inline">xr</ins> id="minimise"/>).</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><figure id="minimise" ></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="minimise" ></div></td>
</tr>
</table>
Kalemanovm
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Gaucher_Disease:_Task_09_-_Structure-based_mutation_analysis&diff=38793&oldid=prev
Kalemanovm: /* Minimise */
2013-09-05T17:46:17Z
<p><span dir="auto"><span class="autocomment">Minimise</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 17:46, 5 September 2013</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 233:</td>
<td colspan="2" class="diff-lineno">Line 233:</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>Another interesting observation is that after reaching the lowest energy in the second minimise iterations in the WT and the foldX mutants, the energy rises constantly in the consequent runs. This probably means that the minimal local energy is reached in the second iteration and then the computation of the gradient at the minimal point can only lead to a higher energy value, maybe to another local minimum with a higher energy. A different pattern happens during the minimisation of the SCWRL mutants: after reaching the local minimal energy already after the first iteration, in the second iteration the energy rises, however it falls a little again in the third iteration, thought not into the same local minimum as in the first iteration. This indicates that a second "suboptimal" local minimum is found. After the forth iteration the energy rises again. </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>Another interesting observation is that after reaching the lowest energy in the second minimise iterations in the WT and the foldX mutants, the energy rises constantly in the consequent runs. This probably means that the minimal local energy is reached in the second iteration and then the computation of the gradient at the minimal point can only lead to a higher energy value, maybe to another local minimum with a higher energy. A different pattern happens during the minimisation of the SCWRL mutants: after reaching the local minimal energy already after the first iteration, in the second iteration the energy rises, however it falls a little again in the third iteration, thought not into the same local minimum as in the first iteration. This indicates that a second "suboptimal" local minimum is found. After the forth iteration the energy rises again. </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="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>We compared the mutant structures in Pymol again after the minimise runs reaching the best energies: after the second round for SQWRL and the first round for foldX (<del class="diffchange diffchange-inline">the</del> <del class="diffchange diffchange-inline">following figure</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>We compared the mutant structures in Pymol again after the minimise runs reaching the best energies: after the second round for SQWRL and the first round for foldX (<ins class="diffchange diffchange-inline"><rx</ins> <ins class="diffchange diffchange-inline">id="minimise"/></ins>).</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="minimise" ></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="minimise" ></div></td>
</tr>
</table>
Kalemanovm
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Gaucher_Disease:_Task_09_-_Structure-based_mutation_analysis&diff=38792&oldid=prev
Kalemanovm: /* Minimise */
2013-09-05T17:42:21Z
<p><span dir="auto"><span class="autocomment">Minimise</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 17:42, 5 September 2013</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 231:</td>
<td colspan="2" class="diff-lineno">Line 231:</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>For the WT, the lowest energy is reached after the first iteration of minimise. This is because the structure is already correct and therefore optimal. Interestingly, the lowest energy of the SQWRL mutants is reached after two minimise iterations, whereas for the foldX mutants the minimal energy is reached already after the first iteration. This may be explained by the fact that foldX already performs a minimisation step. Moreover, foldX minimal energies are always lower, than those calculated by SCWRL.</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>For the WT, the lowest energy is reached after the first iteration of minimise. This is because the structure is already correct and therefore optimal. Interestingly, the lowest energy of the SQWRL mutants is reached after two minimise iterations, whereas for the foldX mutants the minimal energy is reached already after the first iteration. This may be explained by the fact that foldX already performs a minimisation step. Moreover, foldX minimal energies are always lower, than those calculated by SCWRL.</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="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>Another interesting observation is that after reaching the lowest energy in the second minimise iterations in the WT and the foldX mutants, the energy rises constantly in the consequent runs. This probably means that the minimal local energy is reached in the second iteration and then the computation of the gradient at the minimal point can only lead to a higher energy value, maybe to another local minimum with a higher energy. A different pattern happens during the minimisation of the SCWRL mutants: after reaching the local minimal energy already after the first iteration, in the second iteration the energy rises, <del class="diffchange diffchange-inline">but in the third iteration</del> it falls a little again, <del class="diffchange diffchange-inline">but</del> not into the same local minimum as in the first iteration<del class="diffchange diffchange-inline">,</del> <del class="diffchange diffchange-inline">indicating</del> that a second "suboptimal" local minimum is found. After the forth iteration the energy rises again. </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>Another interesting observation is that after reaching the lowest energy in the second minimise iterations in the WT and the foldX mutants, the energy rises constantly in the consequent runs. This probably means that the minimal local energy is reached in the second iteration and then the computation of the gradient at the minimal point can only lead to a higher energy value, maybe to another local minimum with a higher energy. A different pattern happens during the minimisation of the SCWRL mutants: after reaching the local minimal energy already after the first iteration, in the second iteration the energy rises, <ins class="diffchange diffchange-inline">however</ins> it falls a little again<ins class="diffchange diffchange-inline"> in the third iteration</ins>, <ins class="diffchange diffchange-inline">thought</ins> not into the same local minimum as in the first iteration<ins class="diffchange diffchange-inline">. This</ins> <ins class="diffchange diffchange-inline">indicates</ins> that a second "suboptimal" local minimum is found. After the forth iteration the energy rises again. </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>We compared the mutant structures in Pymol again after the minimise runs reaching the best energies: after the second round for SQWRL and the first round for foldX (the following figure).</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>We compared the mutant structures in Pymol again after the minimise runs reaching the best energies: after the second round for SQWRL and the first round for foldX (the following figure).</div></td>
</tr>
</table>
Kalemanovm