Workflow homology modelling glucocerebrosidase

Detailed workflow of the different homology modelling approaches for glucocerebrosidase. Return to overview.

MODELLER

Preparation of the Alignment File

1. Save target protein sequence in PIR-format: target.pir
2. Save PDB-file of template sequence: template:pdb

   If PDB-file consists of several chains: split pdb file with the help of splitpdb (note that minor changes are needed, so that ATOM coordinates get listed in the resulting PDB-file instead of HETATOMS).

3. Run the following Python script with command 'mod9.9 align.py' to create a target-template alignment in PIR-format:

log.verbose()
env = environ()
aln = alignment(env)
mdl= model(env, file='template')
aln.append_model(mdl, align_codes='template')
aln.append(file='target.pir', align_codes=('target'))
aln.align(gap_penalties_1d=(-600,-400))
aln.write(file='target_template.ali', alignment_format='PIR')
aln.write(file='target_template.pap', alignment_format='PAP')

Modelling of the Target Structure

1. Run the following Python script with command 'mod9.9 model.py' to model the structure of the target sequence:

   Note that all files (alignment- and structure file) must be in the same folder

from modeller.automodel import *
log.verbose()
env = environ()
env.io.atom_files_directory = 
a = automodel (env, alnfile = 'TARGET_TEMPLATE.ali', knowns = 'TEMPLATE', sequence = 'TARGET')
a.starting_model = 1
a.ending_model = 1
a.make()

I-TASSER

• Webserver: http://zhanglab.ccmb.med.umich.edu/I-TASSER/
• Input: protein sequence in FASTA-format.

SWISS-MODELLER

Automated Mode

• Webserver: http://swissmodel.expasy.org/workspace/index.php?func=modelling_simple1
• Input: Sequence in fasta format

The automated mode should only be used, if target and template share more than 50% of sequence identity.

Alignment Mode

• Webserver: http://swissmodel.expasy.org/workspace/index.php?func=modelling_align1
• Input: Target-Template Alignment in different formats (FASTA, CLUSTALW, ...)

To create the Alignments needed as input, the tool ClustalW2 was used in this case.