Lab journal task 5

From Bioinformatikpedia

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


-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 was executed online and the 'Automatic Modelling Mode' was used. In the advanced options, we specified the different templates.


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.