Workflow homology modelling glucocerebrosidase

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 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:

from modeller.automodel import * 

log.verbose()

env = environ()

env.io.atom_files_directory = 

a = automodel (env, alnfile = '1OGS_2NT0.ali', knowns = '2NT0', sequence = '1OGS')

a.starting_model = 1

a.ending_model = 1

a.make()