Lab Journal of Task 5 (MSUD)
Calculation of models
Structure models were build with the following programs, using 2BFE and 3EXG as templates.
We have written a Python script Modeller.py which is a wrapper for the original modeller program. It automatically calls modeller and generates models using single or multiple templates.
Single template modelling
For single template modelling, we have used the structure 2BFE (99% sequence identity to 1U5B) and 3EXG (24.9% sequence identity to 1U5B). Computed models are stored in the directory /mnt/home/student/weish/master-practical-2013/task05/models on the student server.
Multiple template modelling
In order to evaluate the performance of homology modelling, we have also tried to use multiple structures with homologous sequence as templates for structure prediction. The Python program create_dataset.py (Task_2_lab_journal_(MSUD)#Dataset_creation) was used for searching for homologous PDB structures with high and low sequence identities.
Swissmodel was run on this server. The models are stored in
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
Evaluation of models
The calculated models were compared to the reference structure 1U5B. Since the residue numbering in the 1U5B pdb file did not fit the query protein sequence of BCKDHA, we used the following script to change the numbering in the pdb file.
<source lang="python"> Change residue numbering in pdb file by adding an offset.
Usage: python change_residue_numbering.py <pdb file> <chain> <offset> <output file>
@author: Laura Schiller
pdb_file = open(sys.argv) out_file = open(sys.argv, "w") chain = sys.argv offset = int(sys.argv)
line = pdb_file.readline() while(line):
if (line.startswith("ATOM") or line.startswith("TER")) and line[21:22] == chain: number = int(line[23:26]) + offset new_line = "%s%3d%s" % (line[0:23], number, line[26:len(line)]) out_file.writelines(new_line) else: out_file.writelines(line) line = pdb_file.readline()
pdb_file.close() out_file.close() </source>
For calculating GDT_TS values, the LGA server was used with options
-3 -sda -ch1:A -ch2:A.
RMSD values were calculated on the SAP server.