Difference between revisions of "Team:NU Kazakhstan/Model"
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<p>We have first started by looking at similar proteins in the Databank. We started with a Blast Search against all PDB proteins. We found two main homologs. The Sulfide: Quinone Reductase of Acidothiobacillus ferrooxidans and that of the hyperthermophile Aquifex Aeolicus. </p> | <p>We have first started by looking at similar proteins in the Databank. We started with a Blast Search against all PDB proteins. We found two main homologs. The Sulfide: Quinone Reductase of Acidothiobacillus ferrooxidans and that of the hyperthermophile Aquifex Aeolicus. </p> | ||
<br> | <br> | ||
| − | <img src="https://static.igem.org/mediawiki/2018/a/ad/T--NU_Kazakhstan--modelling.jpg" class="img-fluid"> | + | <img src="https://static.igem.org/mediawiki/2018/a/ad/T--NU_Kazakhstan--modelling.jpg" class="img-fluid"><br> |
| + | <center>Figure 1. Blast search</center> | ||
| + | <p> | ||
| + | We have then used MODELLER Software to align the protein from A. Aeolicus as the template to our target sequence from Leptolyngbya Hensonii. (please see data in the supporting information). Upon comparing the DOPE (Discrete Optimized Protein Energy) profiles, we noticed that there are regions of clear discrepancies. We have chosen the best five models to compare, this is the comparison for the best model we have. | ||
| + | </p><br> | ||
| + | <img src="https://static.igem.org/mediawiki/2018/d/d9/T--NU_Kazakhstan--modelling2.png" class="img-fluid"> | ||
</div> | </div> | ||
</div> | </div> | ||
Revision as of 12:55, 17 October 2018
We have first started by looking at similar proteins in the Databank. We started with a Blast Search against all PDB proteins. We found two main homologs. The Sulfide: Quinone Reductase of Acidothiobacillus ferrooxidans and that of the hyperthermophile Aquifex Aeolicus.
We have then used MODELLER Software to align the protein from A. Aeolicus as the template to our target sequence from Leptolyngbya Hensonii. (please see data in the supporting information). Upon comparing the DOPE (Discrete Optimized Protein Energy) profiles, we noticed that there are regions of clear discrepancies. We have chosen the best five models to compare, this is the comparison for the best model we have.
