Lab Journal of Task 5 (MSUD)

Calculation of models

Structure models were build with the following programs, using 2BFE and 3EXG as templates.

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.

RMSD

RMSD values were calculated on the SAP server.