MSUP-task7-journal

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-pos	pdb-pos-mapping
N71S	N21S
M82I	M32I
Q125E	Q75E
I213T	I158T
C258Y	C203Y
T310R	T255R
A328T	A273T
I361V	I285V
N404S	N326S
R429H	R351H

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.

Gromacs

repairPDB

USAGE: repairPDB <PDB FILE> [<RANGE>] [<CHAIN:] [<CHAIN:RANGE>] [OPTIONS] OPTIONS: [-offset value] offset the residue numbering

         [-chain char]   change Chain ID
         [-ratom]        renumber Atoms
         [-rres]         renumber Residues
         [-noh]          remove hydrogens
         [-het]          do not change HETATM to ATOM for AA
         [-seq]          protein sequence from AA
         [-seqrs]        protein sequence from SEQRES entries

         [-jprot]        just Protein OR
         [-nohoh]        no water OR
         [-ssw cutoff]   print only waters with B-value below cutoff OR
         [-cleansol]     remove overlapping solvent for GROMACS

         [-dna]          print DNA only OR
         [-nodna]        do not print DNA

SCWRL

resulting sequence:

sslddkpqfpgasaefidklefiqpnvisgipiyrvmdrqgqiinpsedphlpkekvlklyksmtllntmdril
yesqrqgrisfymtnygeegthvgsaaaldntdlvfgqyreagvlmyrdyplelfmaqcygnisdlgkgrqmpv
hygckerhfvtissplatqipqavgaayaakrananrvvicyfgegaasegdahagfnfaatlecpiiffcrnn
gyaistptseqyrgdgiaargpgygimsirvdgndvfavynatkearrravaenqpflieamtyrighhstsdd
ssayrsvdevnywdkqdhpisrlrhyllsqgwwdeeqekawrkqsrrkvmeafeqaerkpkpnpnllfsdvyqe
mpaqlrkqqeslarhlqtygehypldhfdk