Difference between revisions of "Task 5: Homology Modeling"
From Bioinformatikpedia
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<figtable id="Modeller single"> |
<figtable id="Modeller single"> |
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{|class="colBasic2" |
{|class="colBasic2" |
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| − | ! Template || Seq. identity || colspan="2" | std Alignment || colspan="2" | 2d alignment ||colspan="2" | |
+ | ! Template || Seq. identity || colspan="2" | std Alignment || colspan="2" | 2d alignment ||colspan="2" | curated Alignment |
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|- |
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! || || GDT score || RMSD || GDT score || RMSD || GDT score || RMSD |
! || || GDT score || RMSD || GDT score || RMSD || GDT score || RMSD |
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| − | | 1QVO_A || 39% |
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| − | | |
+ | | 1QVO_A || 39% || || || || || || |
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| − | | |
+ | | 1S7X_A || 29% || || || || || || |
| + | |- |
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| − | |+ style="caption-side: bottom; text-align: left" |<font size=2>'''Table 1:'''Template structures and their sequence identity to the target, as reported by Blast. |
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| + | | 1cd1_A || 21% || || || || || || |
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| + | |+ style="caption-side: bottom; text-align: left" |<font size=1.5>'''Table 1:'''Template structures and their sequence identity to the target, as computed by Blast. |
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</figtable> |
</figtable> |
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Revision as of 21:24, 25 August 2013
1A6Z chain A was used as modeling target in all three methods.
Modeller
We used Modeller to create models based on a single template and multiple templates.
Single template
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<figtable id="Modeller single">
| Template | Seq. identity | std Alignment | 2d alignment | curated Alignment | |||
|---|---|---|---|---|---|---|---|
| GDT score | RMSD | GDT score | RMSD | GDT score | RMSD | ||
| 1QVO_A | 39% | ||||||
| 1S7X_A | 29% | ||||||
| 1cd1_A | 21% | ||||||
</figtable>
<xr id="Modeller single"/> list the selected templates and the results of the different
MSA:
| "close" homology | |
| 1rjz_D | 0.34 |
| 1zag_A | 0.36 |
| 1QVO_A | 0.39 |
| distant homology: | |
| 3huj_C | 0.23 |
| 1cd1_A | 0.21 |
| 1VZY_A | 0.14 |
| MIX: |
| 1cd1_A 0.21 |
| 1QVO_A 0.39 |
