Structure-based mutation analysis BCKDHA
The following table presents the PDB structures for BCKDHA to date:
|PDB id||resolution [Å]||R-factor||coverage||ph-value|
The following PDB Structure was chosen because of its good experimental resolution: <bold></bold>
Mapping of the mutations on the crystal structure
Before we could use SCWRL we first had to get the sequence of our model: repairPDB bckdha.pdb -seq >> bckdha.seq
When we have the sequence we have to make one file for each mutation. In these files we copied the bckdha.seq and changed the sequence to lower case letters. Then we add the mutation in an upper case letter.
To run SCWRL we used the command: scwrl -i bckdha.pdb -s mutation1.seq -o mutation1Model.pdb
Total minimal energy of the graph
The fetch-pdb script first checks, if it was called with an valid PDB-id. If the entered PDB code has 4letters, the script tries to download the pdb-file from the server. The successfully downloaded folder gets unzipped and everything except the actual pdb file is removed.
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