Difference between revisions of "Fabry:Structure-based mutation analysis/Journal"

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(→‎Create mutation)
(→‎Create mutation)
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== Create mutation ==
  
== Create mutation ==
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The mutated sequences that were used as input for SCWRL were generated by the script [https://dl.dropbox.com/u/13796643/fabry/strucbased/scripts/scwrl_generate_mutation_sequences.sh.html scwrl_generate_mutation_sequences.sh] which again uses the perl script [https://dl.dropbox.com/u/13796643/fabry/strucbased/scripts/scwrl_mutate_sequence.pl.html scwrl_mutate_sequence.pl] for the actual mutation change.
 +
The mutated sequences that were used as input for SCWRL were generated by the script [https://dl.dropbox.com/u/13796643/fabry/strucbased/scripts/scwrl_generate_mutation_sequences.sh.html scwrl_generate_mutation_sequences.sh] which again uses the perl script [https://dl.dropbox.com/u/13796643/fabry/strucbased/scripts/scwrl_mutate_sequence.pl.html scwrl_mutate_sequence.pl] for the actual mutation change. Afterwards, the models were calculated using [https://dl.dropbox.com/u/13796643/fabry/strucbased/scripts/scwrl_calculate_models.sh.html scwrl_calculate_models.sh].
   
 
bash [https://dl.dropbox.com/u/13796643/fabry/strucbased/scripts/scwrl_generate_mutation_sequences.sh.html scwrl_generate_mutation_sequences.sh]
  
bash [https://dl.dropbox.com/u/13796643/fabry/strucbased/scripts/scwrl_generate_mutation_sequences.sh.html scwrl_generate_mutation_sequences.sh]

Revision as of 22:37, 21 June 2012

Fabry Disease » Structure-based mutation analysis  » Journal

Preparation


Vizualisation

Create mutation

The mutated sequences that were used as input for SCWRL were generated by the script scwrl_generate_mutation_sequences.sh which again uses the perl script scwrl_mutate_sequence.pl for the actual mutation change. Afterwards, the models were calculated using scwrl_calculate_models.sh. 

bash scwrl_generate_mutation_sequences.sh
bash scwrl_calculate_models.sh

Comparison energies

foldX

ln -sf /opt/SS12-Practical/foldx/rotabase.txt
wget http://www.rcsb.org/pdb/files/3S5Y.pdb
perl ../repairPDB 3S5Y.pdb > 3S5Y_repaired.pdb 
/opt/SS12-Practical/foldx/FoldX.linux64 -runfile run.txt

Minimise

bash call_minimise.sh

Gromacs

bash gromacs_mutations.sh ../scwrl/models/*
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