Difference between revisions of "CD task4 protocol"

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=Template identification=
  +
  +
[https://www.dropbox.com/s/x1f9707hm0wgh2d/HHPred.out HHPred output]
 
=Modeller=
 
=Modeller=
   
We modified the scripts provided by the [[Using_Modeller_for_TASK_4 | tutorial]]: [https://www.dropbox.com/s/un3vvkpn9ig5uzw/1_align.py.txt 1_align.py] to suit our demands.
+
We modified the scripts provided in the [[Using_Modeller_for_TASK_4 | tutorial]] to suit our demands.
  +
  +
==Target==
  +
  +
The sequence of out target Aspartoacylase saved in .pir format:
  +
  +
>P1;p45381
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sequence:p45381:::::::0.00: 0.00
  +
MTSCHIAEEHIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKK
  +
CTRYIDCDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTS
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NMGCTLILEDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVG
  +
PQPQGVLRADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIA
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AIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTK
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LTLNAKSIRCCLH*
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  +
==Alignment==
  +
  +
Example alignment script for creating the pairwise alignment of 2GU2 and Aspa.
  +
  +
from modeller import *
  +
env = environ()
  +
# env.io.atom_files_directory = ["/apps/modeller9.9/bin/examples/commands/", "/path/to/your/files/"] ## o$
  +
aln = alignment(env)
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mdl = model(env, file='2GU2', model_segment=('FIRST:A', 'END:A'))
  +
aln.append_model(mdl, align_codes='2GU2', atom_files='2GU2')
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aln.append(file='../p45381.pir', align_codes='p45381')
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aln.align2d()
  +
aln.check()
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aln.write(file='aspa_2gu2-2d.ali', alignment_format='PIR')
  +
aln.malign()
  +
aln.check()
  +
aln.write(file='aspa_2gu2.ali', alignment_format='PIR')
  +
  +
==Single template modelling==
  +
  +
Example alignment script for creating a model of Aspartoacylase from a single template 2GU2:A.
  +
  +
from modeller import *
  +
from modeller.automodel import *
  +
log.verbose()
  +
env = environ()
  +
# env.io.atom_files_directory = ["/apps/modeller9.9/bin/examples/commands/", "/path/to/your/files/"] ## only needed in the VirtualBox
  +
a = automodel(env,
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alnfile = 'aspa_2gu2-2d.ali',
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knowns = '2GU2A',
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sequence = 'p45381',
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assess_methods=(assess.DOPE, assess.GA341))
  +
a.starting_model= 1
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a.ending_model = 1
  +
a.make()
  +
  +
==Alignments for different templates==
  +
  +
  +
<table>
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<tr>
  +
<td>2GU2</td>
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<td><figure id="2gu2_align">[[File:modeller_2gu2_align.png]]</figure></td>
  +
</tr>
  +
  +
<tr>
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<td>3NFZ</td>
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<td><figure id="3nfz_align">[[File:modeller_3nfz_align.png]]</figure></td>
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</tr>
  +
  +
</table>
  +
  +
==Scores==
  +
  +
<b>2GU2</b>
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Filename molpdf DOPE score GA341 score
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----------------------------------------------------------------------
  +
p45381.B99990001.pdb 1640.80847 -36987.52734 1.00000
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  +
= I-Tasser =
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  +
== C Score ==
  +
C-score is a confidence score for estimating the quality of predicted models by I-TASSER. It is calculated
  +
based on the significance of threading template alignments and the convergence parameters of the structure
  +
assembly simulations. C-score is typically in the range of [-5,2], where a C-score of higher value signifies
  +
a model with a high confidence and vice-versa.
   
  +
==Template > 80% Seq Id: 2GU2 (Rattus Norvegicus)==
==Default settings==
 
  +
For the > 80% sequence identity template, we used default values, simply providing the template identifier 2GU2 and Chain A for modelling.

Latest revision as of 15:32, 28 August 2012

Template identification

HHPred output

Modeller

We modified the scripts provided in the tutorial to suit our demands.

Target

The sequence of out target Aspartoacylase saved in .pir format:

>P1;p45381
sequence:p45381:::::::0.00: 0.00
MTSCHIAEEHIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKK
CTRYIDCDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTS
NMGCTLILEDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVG
PQPQGVLRADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIA
AIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTK
LTLNAKSIRCCLH*

Alignment

Example alignment script for creating the pairwise alignment of 2GU2 and Aspa.

from modeller import *
env = environ()
# env.io.atom_files_directory = ["/apps/modeller9.9/bin/examples/commands/", "/path/to/your/files/"] ## o$
aln = alignment(env)
mdl = model(env, file='2GU2', model_segment=('FIRST:A', 'END:A'))
aln.append_model(mdl, align_codes='2GU2', atom_files='2GU2')
aln.append(file='../p45381.pir', align_codes='p45381')
aln.align2d()
aln.check()
aln.write(file='aspa_2gu2-2d.ali', alignment_format='PIR')
aln.malign()
aln.check()
aln.write(file='aspa_2gu2.ali', alignment_format='PIR')

Single template modelling

Example alignment script for creating a model of Aspartoacylase from a single template 2GU2:A.

from modeller import *
from modeller.automodel import *    
log.verbose()   
env = environ() 
# env.io.atom_files_directory = ["/apps/modeller9.9/bin/examples/commands/", "/path/to/your/files/"] ## only needed in the VirtualBox
a = automodel(env,
            alnfile  = 'aspa_2gu2-2d.ali',   
            knowns   = '2GU2A',              
            sequence = 'p45381',
            assess_methods=(assess.DOPE, assess.GA341))
a.starting_model= 1                
a.ending_model  = 1                
a.make()

Alignments for different templates

2GU2 <figure id="2gu2_align">Modeller 2gu2 align.png</figure>
3NFZ <figure id="3nfz_align">Modeller 3nfz align.png</figure>

Scores

2GU2

Filename                          molpdf     DOPE score    GA341 score
----------------------------------------------------------------------
p45381.B99990001.pdb          1640.80847   -36987.52734        1.00000

I-Tasser

C Score

C-score is a confidence score for estimating the quality of predicted models by I-TASSER. It is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5,2], where a C-score of higher value signifies a model with a high confidence and vice-versa.

Template > 80% Seq Id: 2GU2 (Rattus Norvegicus)

For the > 80% sequence identity template, we used default values, simply providing the template identifier 2GU2 and Chain A for modelling.