Difference between revisions of "MSUP-task7-journal"

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Line 4: Line 4:
   
 
sequence mutated:
  
sequence mutated:
  +
kpqfpgasaefidklefiqpSvisgipiyrvIdrqgqiinpsedphlpkekvlklyksmtll
−
kpqfpgasaefidklefiqpSvisgipiyrvIdrqgqiinpsedphlp
  
  +
ntmdrilyesqrEgrisfymtnygegtvgsaaaldntdlvfgareagvlmyrdyplelfmaq
−
kekvlklyksmtllntmdrilyesqrEgrisfymtnygegtvgsaaal
  
  +
cygnisdlgkgrqpvygckerhfvtissplatqTpqavgaayaakrananrvvicyfgegaa
−
dntdlvfgareagvlmyrdyplelfmaqcygnisdlgkgrqpvygcke
  
  +
segdahagfnfaatleYpiiffcrnngyaistptseqyrgdgiaargpgygimsirvdgndv
−
rhfvtissplatqTpqavgaayaakrananrvvicyfgegaasegdah
  
  +
favynaRkearrravaenqpflieTmtyrigstdhpVsrlrhylqgwwdeeqekawrkqsrr
−
agfnfaatleYpiiffcrnngyaistptseqyrgdgiaargpgygims
  
  +
kvmeafeqaerkpkpSpnllfsdvyqempaqlrkqqeslaHhlqtygehypldhfdk
−
irvdgndvfavynaRkearrravaenqpflieTmtyrigstdhpVsrl
  
  +
−
rhylqgwwdeeqekawrkqsrrkvmeafeqaerkpkpSpnllfsdvyq
  
  +
posmap:
−
empaqlrkqqeslaHhlqtygehypldhfdK
  
  +
  +
<table border=1>
  +
<tr><td>snp-pos</td><td>pdb-pos-mapping</td></tr>
  +
<tr><td>N71S</td><td>N21S</td></tr>
  +
<tr><td>M82I</td><td>M32I</td></tr>
  +
<tr><td>Q125E</td><td>Q75E</td></tr>
  +
<tr><td>I213T</td><td>I158T</td></tr>
  +
<tr><td>C258Y</td><td>C203Y</td></tr>
  +
<tr><td>T310R</td><td>T255R</td></tr>
  +
<tr><td>A328T</td><td>A273T</td></tr>
  +
<tr><td>I361V</td><td>I285V</td></tr>
  +
<tr><td>N404S</td><td>N326S</td></tr>
  +
<tr><td>R429H</td><td>R351H</td></tr>
  +
</table>
  +
  +
Commad for SCWRL4:
  +
/opt/SS12-Practical/scwrl4/Scwrl4 -i 2bfd_A.ent -s BCKDHA_2bfd_a.sequence_final -o model_OUT.pdb
  +
  +
== FoldX ==
  +
{|class="wikitable" border="1" style="border-spacing:0;text-align: center;"
  +
|-
  +
! 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

Latest revision as of 20:45, 25 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

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
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