Difference between revisions of "Workflow homology modelling glucocerebrosidase"
From Bioinformatikpedia
(→Modelling of the Target Structure) |
(→Preparation of the Alignment File) |
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=== Preparation of the Alignment File === |
=== Preparation of the Alignment File === |
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| − | # Save target protein sequence in PIR-format: |
+ | # Save target protein sequence in PIR-format: TARGET.pir |
| − | # Save PDB-file of template sequence: |
+ | # Save PDB-file of template sequence: TEMPLATE.pdb |
#: If PDB-file consists of several chains: split pdb file with the help of [http://structure.usc.edu/splitpdb/ splitpdb] (note that minor changes are needed, so that ATOM coordinates get listed in the resulting PDB-file instead of HETATOMS). |
#: If PDB-file consists of several chains: split pdb file with the help of [http://structure.usc.edu/splitpdb/ splitpdb] (note that minor changes are needed, so that ATOM coordinates get listed in the resulting PDB-file instead of HETATOMS). |
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# Run the following Python script with command '<code>mod9.9 align.py</code>' to create a target-template alignment in PIR-format: |
# Run the following Python script with command '<code>mod9.9 align.py</code>' to create a target-template alignment in PIR-format: |
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env = environ() |
env = environ() |
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aln = alignment(env) |
aln = alignment(env) |
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| − | mdl= model(env, file=' |
+ | mdl= model(env, file='TEMPLATE') |
| − | aln.append_model(mdl, align_codes=' |
+ | aln.append_model(mdl, align_codes='TEMPLATE') |
| − | aln.append(file=' |
+ | aln.append(file='TARGET.pir', align_codes=('TARGET')) |
aln.align(gap_penalties_1d=(-600,-400)) |
aln.align(gap_penalties_1d=(-600,-400)) |
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| − | aln.write(file=' |
+ | aln.write(file='TARGET_TEMPLATE.ali', alignment_format='PIR') |
| − | aln.write(file=' |
+ | aln.write(file='TARGET_TEMPLATE.pap', alignment_format='PAP')</code> |
=== Modelling of the Target Structure === |
=== Modelling of the Target Structure === |
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Revision as of 11:59, 11 June 2011
Detailed workflow of the different homology modelling approaches for glucocerebrosidase. Return to overview.
Contents
MODELLER
Preparation of the Alignment File
- Save target protein sequence in PIR-format: TARGET.pir
- 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).
- 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
- 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.
