Fabry:Structure-based mutation analysis/Journal

Fabry Disease » Structure-based mutation analysis  » Journal

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Vizualisation

The mapping of all SNPs was done with the bash script map_mark_positions.sh

bash map_mark_positions.sh

It creates the script map.pml, which can be loaded in pymol. The resulting 30 png pictures were merged into an animated gif with convert.

convert -delay 80 *.png map.gif

Create mutation

Pymol

The mutations were introduced on the basis of an backbone independent rotamer library to show the difference to the backbone dependent library used in SCWRL. The pictures were created with the pymol scripts mutSingle.pml and surface.pml

SCWRL4

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. The available options for SCWRL can be found here.

bash scwrl_generate_mutation_sequences.sh
bash scwrl_calculate_models.sh

An additional run without any mutation was also done.

Scwrl4 -h -s scwrl/sequence.fasta -i 3S5Y_chainA_repaired.pdb -o wt.pdb > wt.log

Afterwards the minimal energies were parsed from the logfiles and compared to the minimal energy of the wildtype.

perl parseEnergySCWRL.pl

The pictures were again created with pymol on the basis of the .pdb files created by SCWRL4 and the pymol script scwrl.pml

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

We created the input files according to the example: run.txt, list.txt and individual_list.txt

Scores were used from the output files Raw_BuildModel_3S5Y_repaired.fxout and Dif_BuildModel_3S5Y_repaired.fxout and compared to the wildtype energies.

Again, the pictures were created with pymol on the basis of the .pdb files created by FoldX and the pymol script scwrl.pml

Minimise

bash call_minimise.sh

The energies were extracted with

perl parseEnergy.pl

Afterwards plots were created

Rscript plotEnergy.R

and example pictures made with pymol its.pml

Gromacs

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