Difference between revisions of "Lab Journal of Task 5 (MSUD)"
From Bioinformatikpedia
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=== Swissmodel === |
=== Swissmodel === |
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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> |
+ | 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 === |
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| − | [http://zhanglab.ccmb.med.umich.edu/I-TASSER/ 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. |
+ | [http://zhanglab.ccmb.med.umich.edu/I-TASSER/ 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. Models are stored in <code>/mnt/home/student/schillerl/MasterPractical/task5/iTasser/</code>. |
== Evaluation of models == |
== Evaluation of models == |
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Revision as of 13:40, 8 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. Models are stored in /mnt/home/student/schillerl/MasterPractical/task5/iTasser/.
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.
RMSD
RMSD values were calculated on the SAP server.
