Difference between revisions of "Task 5: Homology Modeling"
From Bioinformatikpedia
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[[lab journal task 5]] |
[[lab journal task 5]] |
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| + | 1A6Z chain A was used as modeling target in all three methods. |
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==Modeller== |
==Modeller== |
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| + | We used Modeller to create models based on a single template and multiple templates. |
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=== Single template === |
=== Single template === |
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| + | <css> |
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| − | Target: 1A6Z chain A |
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| + | table.colBasic2 { |
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| + | margin-left: auto; |
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| + | margin-right: auto; |
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| + | border: 2px solid black; |
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| + | border-collapse:collapse; |
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| + | width: 70%; |
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| + | } |
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| + | .colBasic2 th,td { |
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| + | padding: 3px; |
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| + | border: 2px solid black; |
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| + | } |
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| + | .colBasic2 td { |
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| + | text-align:left; |
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| + | } |
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| + | .colBasic2 tr th { background-color:#efefef; color: black;} |
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| + | .colBasic2 tr:first-child th { background-color:#adceff; color:black;} |
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| + | </css> |
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| + | <figtable id="Modeller single"> |
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| − | {| |
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| + | {|class="colBasic2" |
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| − | | Template || SeqID || std Alignment || 2d alignment || curated Alignment |
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| + | ! 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 |
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| − | | 1QVO_A || 0.39 |
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| + | | 1QVO_A || 39% |
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|- |
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| − | | 1S7X_A || |
+ | | 1S7X_A || 29% |
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| − | | 1cd1_A || |
+ | | 1cd1_A || 21% |
| + | |+ 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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| + | </figtable> |
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| + | <xr id="Modeller single"/> list the selected templates and the results of the different |
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Revision as of 22:23, 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
<css> table.colBasic2 { margin-left: auto; margin-right: auto; border: 2px solid black; border-collapse:collapse; width: 70%; } .colBasic2 th,td { padding: 3px; border: 2px solid black; } .colBasic2 td { text-align:left; } .colBasic2 tr th { background-color:#efefef; color: black;} .colBasic2 tr:first-child th { background-color:#adceff; color:black;} </css>
<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 |
