Difference between revisions of "CD task4 protocol"
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| + | =Template identification= |
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| + | |||
| + | [https://www.dropbox.com/s/x1f9707hm0wgh2d/HHPred.out HHPred output] |
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=Modeller= |
=Modeller= |
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| − | We modified the scripts provided |
+ | We modified the scripts provided in the [[Using_Modeller_for_TASK_4 | tutorial]] to suit our demands. |
==Target== |
==Target== |
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PQPQGVLRADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIA |
PQPQGVLRADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIA |
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AIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTK |
AIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTK |
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| − | LTLNAKSIRCCLH |
+ | LTLNAKSIRCCLH* |
| + | ==Alignment== |
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| + | Example alignment script for creating the pairwise alignment of 2GU2 and Aspa. |
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| + | from modeller import * |
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| + | env = environ() |
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| + | # env.io.atom_files_directory = ["/apps/modeller9.9/bin/examples/commands/", "/path/to/your/files/"] ## o$ |
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| + | aln = alignment(env) |
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| + | mdl = model(env, file='2GU2', model_segment=('FIRST:A', 'END:A')) |
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| + | 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() |
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| + | aln.check() |
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| + | aln.write(file='aspa_2gu2-2d.ali', alignment_format='PIR') |
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| + | aln.malign() |
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| + | aln.check() |
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| + | aln.write(file='aspa_2gu2.ali', alignment_format='PIR') |
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| + | ==Single template modelling== |
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| + | Example alignment script for creating a model of Aspartoacylase from a single template 2GU2:A. |
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| + | from modeller import * |
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| + | from modeller.automodel import * |
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| + | log.verbose() |
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| + | env = environ() |
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| + | # env.io.atom_files_directory = ["/apps/modeller9.9/bin/examples/commands/", "/path/to/your/files/"] ## only needed in the VirtualBox |
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| + | 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)) |
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| + | a.starting_model= 1 |
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| + | a.ending_model = 1 |
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| + | a.make() |
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| + | ==Alignments for different templates== |
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| − | ==Alignment== |
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| + | |||
| + | |||
| + | <table> |
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| + | <tr> |
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| + | <td>2GU2</td> |
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| + | <td><figure id="2gu2_align">[[File:modeller_2gu2_align.png]]</figure></td> |
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| + | </tr> |
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| + | |||
| + | <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> |
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| + | |||
| + | </table> |
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| + | |||
| + | ==Scores== |
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| + | |||
| + | <b>2GU2</b> |
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| + | Filename molpdf DOPE score GA341 score |
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| + | ---------------------------------------------------------------------- |
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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 == |
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| + | C-score is a confidence score for estimating the quality of predicted models by I-TASSER. It is calculated |
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| + | based on the significance of threading template alignments and the convergence parameters of the structure |
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| + | assembly simulations. C-score is typically in the range of [-5,2], where a C-score of higher value signifies |
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| + | a model with a high confidence and vice-versa. |
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| + | ==Template > 80% Seq Id: 2GU2 (Rattus Norvegicus)== |
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| − | ==Default settings== |
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| + | For the > 80% sequence identity template, we used default values, simply providing the template identifier 2GU2 and Chain A for modelling. |
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Latest revision as of 14:32, 28 August 2012
Contents
Template identification
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"> </figure> |
| 3NFZ | <figure id="3nfz_align"> </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.
