Difference between revisions of "Lab Journal of Task 5 (MSUD)"
From Bioinformatikpedia
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=== GDT === |
=== GDT === |
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| − | For calculating GDT_TS values, the [http://proteinmodel.org/AS2TS/LGA/lga.html LGA] server was used with |
+ | For calculating GDT_TS values, the [http://proteinmodel.org/AS2TS/LGA/lga.html LGA] server was used with options <code>-3 -sda -ch1:A -ch2:A</code>. |
=== RMSD === |
=== RMSD === |
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Revision as of 16:45, 7 June 2013
Contents
Calculation of models
Structure models were build with the following programs, using 2BFE and 3EXG as templates.
Modeller
Swissmodel
Swissmodel was run on this server. The models are stored in /mnt/home/student/schillerl/MasterPractical/task5/Swissmodel/
iTasser
This server was used for running iTasser. For creating a model with the low sequence identity template (3EXG), "Option II" was set to exclude templates with more than 30 % sequence identity from the iTasser template library.
Evaluation of models
The calculated models were compared to the reference structure 1U5B.
GDT
For calculating GDT_TS values, the LGA server was used with options -3 -sda -ch1:A -ch2:A.
