Difference between revisions of "Task 5: Homology Modeling"
From Bioinformatikpedia
| Line 1: | Line 1: | ||
[[lab journal task 5]] |
[[lab journal task 5]] |
||
| + | |||
| + | 1A6Z chain A was used as modeling target in all three methods. |
||
==Modeller== |
==Modeller== |
||
| + | We used Modeller to create models based on a single template and multiple templates. |
||
=== Single template === |
=== Single template === |
||
| + | <css> |
||
| − | Target: 1A6Z chain A |
||
| + | 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"> |
||
| − | {| |
||
| + | {|class="colBasic2" |
||
| − | | Template || SeqID || std Alignment || 2d alignment || curated Alignment |
||
| + | ! Template || Seq. identity || colspan="2" | std Alignment || colspan="2" | 2d alignment ||colspan="2" | curated Alignment |
||
|- |
|- |
||
| + | ! || || GDT score || RMSD || GDT score || RMSD || GDT score || RMSD |
||
| − | | 1QVO_A || 0.39 |
||
| + | | 1QVO_A || 39% |
||
|- |
|- |
||
| − | | 1S7X_A || |
+ | | 1S7X_A || 29% |
|- |
|- |
||
| − | | 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. |
||
|} |
|} |
||
| + | </figtable> |
||
| + | <xr id="Modeller single"/> list the selected templates and the results of the different |
||
Revision as of 21:23, 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 |
