Difference between revisions of "Lab Journal of Task 5 (MSUD)"

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(Evaluation of models)
(Swissmodel)
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=== Swissmodel ===
 
=== Swissmodel ===
   
Swissmodel was run on [http://swissmodel.expasy.org/workspace/index.php?func=modelling_simple1&userid=USERID&token=TOKEN this server].
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Swissmodel was run on [http://swissmodel.expasy.org/workspace/index.php?func=modelling_simple1&userid=USERID&token=TOKEN this server]. The models are stored in <code>/mnt/home/student/schillerl/MasterPractical/task5/Swissmodel/</code>
   
 
=== iTasser ===
 
=== iTasser ===

Revision as of 13:58, 6 June 2013

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 option -3.

RMSD