Difference between revisions of "MSUP-task7-journal"

From Bioinformatikpedia
(Scwrl)
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Commad for SCWRL4:
 
Commad for SCWRL4:
 
/opt/SS12-Practical/scwrl4/Scwrl4 -i 2bfd_A.ent -s BCKDHA_2bfd_a.sequence_final -o model_OUT.pdb
 
/opt/SS12-Practical/scwrl4/Scwrl4 -i 2bfd_A.ent -s BCKDHA_2bfd_a.sequence_final -o model_OUT.pdb
  +
  +
== FoldX ==
  +
For FoldX we used the following Files
  +
  +
== Minimise ==
  +
For minimise we used a slightly adapted version of the [[Task7_Hemochromatosis_Protocol#Minimise]] shell script from the heterochromatisis group.

Revision as of 18:10, 24 June 2012

Scwrl

Sequence extraction from pdb-file:

/opt/SS12-Practical/scripts/repairPDB 2bfd_A.ent -chain A -seq
sequence mutated:
kpqfpgasaefidklefiqpSvisgipiyrvIdrqgqiinpsedphlpkekvlklyksmtll
ntmdrilyesqrEgrisfymtnygegtvgsaaaldntdlvfgareagvlmyrdyplelfmaq
cygnisdlgkgrqpvygckerhfvtissplatqTpqavgaayaakrananrvvicyfgegaa
segdahagfnfaatleYpiiffcrnngyaistptseqyrgdgiaargpgygimsirvdgndv
favynaRkearrravaenqpflieTmtyrigstdhpVsrlrhylqgwwdeeqekawrkqsrr
kvmeafeqaerkpkpSpnllfsdvyqempaqlrkqqeslaHhlqtygehypldhfdk

posmap:

snp-pospdb-pos-mapping
N71SN21S
M82IM32I
Q125EQ75E
I213TI158T
C258YC203Y
T310RT255R
A328TA273T
I361VI285V
N404SN326S
R429HR351H

Commad for SCWRL4:

/opt/SS12-Practical/scwrl4/Scwrl4 -i 2bfd_A.ent -s BCKDHA_2bfd_a.sequence_final -o model_OUT.pdb

FoldX

For FoldX we used the following Files

Minimise

For minimise we used a slightly adapted version of the Task7_Hemochromatosis_Protocol#Minimise shell script from the heterochromatisis group.