MSUP-task7-journal

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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

Mutation total energy Backbone Hbond Sidechain Hbond Van der Waals Electrostatics Solvation Polar Solvation Hydrophobic Van der Waals clashes entropy sidechain entropy mainchain sloop_entropy mloop_entropy cis_bond torsional clash backbone clash helix dipole water bridge disulfide electrostatic kon partial covalent bonds energy Ionisation Entropy Complex
N71S 0.47 0.13 0.13 0.12 0.00 -0.16 0.21 0.00 -0.16 0.20 0.00 0.00 0.00 -0.00 -0.02 0.00 0.00 0.00 0.00 0.00 0.00 0.00
M82I -0.12 -0.00 0.00 0.33 -0.03 -0.15 0.24 0.06 -0.31 -0.39 0.00 0.00 0.00 0.12 0.04 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Q125E 1.50 -0.01 3.18 -0.05 -0.70 -0.04 -0.05 0.15 -1.58 0.07 0.00 0.00 0.00 -0.03 -0.03 0.55 0.00 0.00 0.00 0.00 0.00 0.00
I213T 2.21 -0.38 -0.49 1.04 0.00 0.44 2.54 -0.08 -0.49 -0.38 0.00 0.00 0.00 0.01 -0.44 0.00 0.00 0.00 0.00 0.00 0.00 0.00
C258Y 4.55 0.01 0.17 -1.78 0.07 1.11 -2.84 7.22 0.31 0.01 0.00 0.00 0.00 0.27 0.90 -0.00 0.00 0.00 0.00 0.00 0.00 0.00
T310R 8.51 0.02 0.28 -1.67 0.13 3.01 -1.29 4.89 1.30 0.04 0.00 0.00 0.00 2.22 0.11 -0.42 0.00 0.00 0.00 0.00 0.00 0.00
A328T 2.77 -0.40 -0.41 -0.63 -0.01 1.14 -0.63 2.76 0.51 -0.92 0.00 0.00 0.00 1.36 -0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00
I361V 0.50 0.01 -0.01 0.48 0.00 -0.28 0.86 -0.04 -0.55 0.02 0.00 0.00 0.00 0.01 -0.07 0.00 0.00 0.00 0.00 0.00 -0.01 0.00
N404S 0.20 0.01 0.20 0.37 0.00 -0.48 0.50 -0.02 -0.25 -0.22 0.00 0.00 0.00 0.09 -0.11 0.00 0.00 0.00 0.00 0.00 0.00 0.00
R429H -0.08 -0.14 -0.19 0.37 0.14 -0.50 0.40 0.03 -0.43 0.26 0.00 0.00 0.00 -0.19 -0.20 -0.07 0.00 0.00 0.00 0.00 0.25 0.00

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