Difference between revisions of "Lab journal task 5"
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(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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| − | - computation of |
+ | - computation of GDT score: how did we calculate id? where is the programm from, how did we use it? |
| + | TMscore model.pdb 1a6z_a.pdb |
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| + | |||
- computation of RMSD: how? |
- computation of RMSD: how? |
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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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Revision as of 17:24, 26 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
- computation of GDT score: how did we calculate id? where is the programm from, how did we use it?
TMscore model.pdb 1a6z_a.pdb
- computation of RMSD: how?
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?
