Difference between revisions of "Lab journal task 5"
(Created page with "We used the structure of 1A6Z chain A as target. The templates were selected based on the structures assembled for task 4 and also the Blast alignment from task 2. -selection of…") |
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| − | We used the structure of 1A6Z chain A as target. The templates were selected based on the structures assembled for task 4 and also the Blast alignment from task 2. |
+ | We used the structure of 1A6Z chain A as target. The templates were selected based on the structures assembled for task 4 and also the Blast alignment from task 2. Unfortunatels, we could not find a sequence with a higher sequence identity than 39%. |
-selection of template structures |
-selection of template structures |
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-creation of alignments: sdt and 2d |
-creation of alignments: sdt and 2d |
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| + | The RMSD and GDT score were calculated with TM scoring function of the [http://zhanglab.ccmb.med.umich.edu/TM-score/ Zhang lab]. The function was downloaded and executed with: |
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| − | - computation of TM score: how did we calculate id? where is the programm from, how did we use it? Why did we use TM instead of GDT? |
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| + | TMscore model.pdb 1a6z_a.pdb |
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| − | - computation of RMSD: how? |
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| + | We then extracted the RMSD and GDT_TS score from the output. The GDT score is given as value between 0 and 1. |
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| + | |||
| + | We searched the Blast hits from task 2 to create sets with close and distant homology. We could not find a structure with a higher sequence identity than 39%. |
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| + | |||
| + | - computation of MSA: how? |
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| + | ==Swiss-Model == |
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| + | Swiss-Model was executed online and the 'Automatic Modelling Mode' was used. In the advanced options, we specified the different templates. |
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| + | == I-Tasser == |
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| + | I-Tasser was also used from the web interface. Option I was used to specify a specific template and Option II was used for the low sequence similarity group to exclude sequences with over 30% identity. |
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Latest revision as of 19:07, 27 August 2013
We used the structure of 1A6Z chain A as target. The templates were selected based on the structures assembled for task 4 and also the Blast alignment from task 2. Unfortunatels, we could not find a sequence with a higher sequence identity than 39%.
-selection of template structures
Modeller
-creation of alignments: sdt and 2d
The RMSD and GDT score were calculated with TM scoring function of the Zhang lab. The function was downloaded and executed with:
TMscore model.pdb 1a6z_a.pdb
We then extracted the RMSD and GDT_TS score from the output. The GDT score is given as value between 0 and 1.
We searched the Blast hits from task 2 to create sets with close and distant homology. We could not find a structure with a higher sequence identity than 39%.
- computation of MSA: how?
Swiss-Model
Swiss-Model was executed online and the 'Automatic Modelling Mode' was used. In the advanced options, we specified the different templates.
I-Tasser
I-Tasser was also used from the web interface. Option I was used to specify a specific template and Option II was used for the low sequence similarity group to exclude sequences with over 30% identity.
