Difference between revisions of "Task 5: Homology Modeling"
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| 1S7X_A || 29% || 0.3355|| 15.806|| 0.2509 || 18.099|| || |
| 1S7X_A || 29% || 0.3355|| 15.806|| 0.2509 || 18.099|| || |
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+ | | 1CD1_A || 21% || 0.3640 ||18.066 || 0.4697 || 5.640 || || |
|+ 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). |
|+ 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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<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. The RMSD and TM score are given for all models. The TM score ranges in the interval of (0, 1]. A value below 0.17 indicates a random similarity and a TM score above 0.5 corresponds to two structures with the same fold in CATH or SCOP (see [http://zhanglab.ccmb.med.umich.edu/TM-score/ TM score]). |
<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. The RMSD and TM score are given for all models. The TM score ranges in the interval of (0, 1]. A value below 0.17 indicates a random similarity and a TM score above 0.5 corresponds to two structures with the same fold in CATH or SCOP (see [http://zhanglab.ccmb.med.umich.edu/TM-score/ TM score]). |
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| − | Including the secondary structure information did only improve the |
+ | Including the secondary structure information did only improve the model of the most distant homolog 1CD1_A. |
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Revision as of 22:01, 25 August 2013
1A6Z chain A was used as modeling target for 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% | 0.6241 | 3.647 | 0.5653 | 4.994 | ||
| 1S7X_A | 29% | 0.3355 | 15.806 | 0.2509 | 18.099 | ||
| 1CD1_A | 21% | 0.3640 | 18.066 | 0.4697 | 5.640 | ||
</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. The RMSD and TM score are given for all models. The TM score ranges in the interval of (0, 1]. A value below 0.17 indicates a random similarity and a TM score above 0.5 corresponds to two structures with the same fold in CATH or SCOP (see TM score). Including the secondary structure information did only improve the model of the most distant homolog 1CD1_A.
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 |
