Difference between revisions of "Task 5: Homology Modeling"
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! Template || Seq. identity || colspan="2" | std Alignment || colspan="2" | 2d alignment ||colspan="2" | curated Alignment |
! Template || Seq. identity || colspan="2" | std Alignment || colspan="2" | 2d alignment ||colspan="2" | curated Alignment |
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| − | ! || || |
+ | ! || || TM score || RMSD || TM score || RMSD || TM score || RMSD |
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| 1QVO_A || 39% || || || || || || |
| 1QVO_A || 39% || || || || || || |
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| 1cd1_A || 21% || || || || || || |
| 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. |
+ | |+ 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. The RMSD and TM score are given as a quality measure for the different models based on a pairwise sequence alignment with dynamic programming (std Alignment), pairwise sequence alignment with additional secondary structure information (2d Alignment) and manually curated alignments (curated Alignment). |
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</figtable> |
</figtable> |
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| − | <xr id="Modeller single"/> |
+ | <xr id="Modeller single"/> lists the selected templates and the Modeller results for the different template structures and alignment methods. In addition to the standard pairwise sequence alignment based on dynamic programming, we also used Modeller's alignment.alig2dn() method to improve the alignment by including secondary structure information and improved the alignments manually. |
Revision as of 21:46, 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 | |||
|---|---|---|---|---|---|---|---|
| TM score | RMSD | TM score | RMSD | TM score | RMSD | ||
| 1QVO_A | 39% | ||||||
| 1S7X_A | 29% | ||||||
| 1cd1_A | 21% | ||||||
</figtable>
<xr id="Modeller single"/> lists the selected templates and the Modeller results for the different template structures and alignment methods. In addition to the standard pairwise sequence alignment based on dynamic programming, we also used Modeller's alignment.alig2dn() method to improve the alignment by including secondary structure information and improved the alignments manually.
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 |
