Difference between revisions of "Homology Modeling of ARS A"
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| '' Classical <br> Dynamic Programming '' |
| '' Classical <br> Dynamic Programming '' |
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− | | [[File:1AUK.1P49.png | 200px | center | thumb | real structure of 1P49 and structure of 1AUK modelled by modeller, visualized in Pymol]] |
+ | | [[File:1AUK.1P49.png | 200px | center | thumb | real structure of 1P49 and structure of 1AUK modelled by modeller with tamplate 1P49, visualized in Pymol]] |
− | | [[File:1AUK.2VQR.png | 200px | center | thumb | real structure of 2VQR and structure of 1AUK modelled by modeller, visualized in Pymol]] |
+ | | [[File:1AUK.2VQR.png | 200px | center | thumb | real structure of 2VQR and structure of 1AUK modelled by modeller with tamplate 2VQR, visualized in Pymol]] |
− | | [[File:1AUK.1FSU.png | 200px | center | thumb | real structure of 1FSU and structure of 1AUK modelled by modeller, visualized in Pymol]] |
+ | | [[File:1AUK.1FSU.png | 200px | center | thumb | real structure of 1FSU and structure of 1AUK modelled by modeller with tamplate 1FSU, visualized in Pymol]] |
− | | [[File:1AUK.3ED4.png | 200px | center | thumb | real structure of 3ED4 and structure of 1AUK modelled by modeller, visualized in Pymol]] |
+ | | [[File:1AUK.3ED4.png | 200px | center | thumb | real structure of 3ED4 and structure of 1AUK modelled by modeller with tamplate 3ED4, visualized in Pymol]] |
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| '' Dynamic Programming <br> with structural information <br> from the template'' |
| '' Dynamic Programming <br> with structural information <br> from the template'' |
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− | | [[File:1AUK.1P492d.png | 200px | center | thumb | real structure of 1P49 and structure of 1AUK modelled by modeller, visualized in Pymol]] |
+ | | [[File:1AUK.1P492d.png | 200px | center | thumb | real structure of 1P49 and structure of 1AUK modelled by modeller with tamplate 1P49, visualized in Pymol]] |
− | | [[File:1AUK.2VQR2d.png | 200px | center | thumb | real structure of 2VQR and structure of 1AUK modelled by modeller, visualized in Pymol]] |
+ | | [[File:1AUK.2VQR2d.png | 200px | center | thumb | real structure of 2VQR and structure of 1AUK modelled by modeller with tamplate 2VQR, visualized in Pymol]] |
− | | [[File:1AUK.1FSU2d.png | 200px | center | thumb | real structure of 1FSU and structure of 1AUK modelled by modeller, visualized in Pymol]] |
+ | | [[File:1AUK.1FSU2d.png | 200px | center | thumb | real structure of 1FSU and structure of 1AUK modelled by modeller with tamplate 1FSU, visualized in Pymol]] |
− | | [[File:1AUK.3ED42d.png | 200px | center | thumb | real structure of 3ED4 and structure of 1AUK modelled by modeller, visualized in Pymol]] |
+ | | [[File:1AUK.3ED42d.png | 200px | center | thumb | real structure of 3ED4 and structure of 1AUK modelled by modeller with tamplate 3ED4, visualized in Pymol]] |
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| '' Dynamic Programming <br> with structural information <br> from the template'' |
| '' Dynamic Programming <br> with structural information <br> from the template'' |
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− | | [[File:1AUK.3ED4A2d.png | 200px | center | thumb | real structure of |
+ | | [[File:1AUK.3ED4A2d.png | 200px | center | thumb | real structure of 1AUK and structure of 1AUK modelled by modeller with tamplate 3ED4A, visualized in Pymol]] |
− | | [[File:1AUK.3ED4B2d.png | 200px | center | thumb | real structure of |
+ | | [[File:1AUK.3ED4B2d.png | 200px | center | thumb | real structure of 1AUK and structure of 1AUK modelled by modeller with tamplate 3ED4B, visualized in Pymol]] |
− | | [[File:1AUK.3ED4C2d.png | 200px | center | thumb | real structure of |
+ | | [[File:1AUK.3ED4C2d.png | 200px | center | thumb | real structure of 1AUK and structure of 1AUK modelled by modeller with tamplate 3ED4C, visualized in Pymol]] |
− | | [[File:1AUK.3ED4D2d.png | 200px | center | thumb | real structure of |
+ | | [[File:1AUK.3ED4D2d.png | 200px | center | thumb | real structure of 1AUK and structure of 1AUK modelled by modeller with tamplate 3ED4D, visualized in Pymol]] |
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+ | ==== Modification of Alignments ==== |
Revision as of 11:54, 9 June 2011
Contents
HHpred
We used the webserver and
Modeller
Proteins used as templates
We identified the following proteins (see Alignment TASK) as potential targets for homology modeling:used the following
SeqIdentifier | Seq Identity (from TASK 2) | source | Protein function | True homolog (HSSP) | Seq Identity (pairw. ali.) |
---|---|---|---|---|---|
1P49 | 39.0% | Homo Sapiens | Steryl-Sulfatase | yes | 31.9% |
1FSU | 28.0% | Homo Sapiens | Arylsulfatase B | yes | 26.5% |
2VQR | 20.0% | Rhizobium leguminosarum | Monoester Hydrolase | no | 20.3% |
3ED4 | 32.0% | Escherichia coli | Arylsulfatase | yes | 27.7% |
Our potential templates, identified by the database searches contain all homologs with known structure, regarding to HSSP.
Single template modelling
In order to predict the structure using a single template structure, modeller needs pairwise sequence alignments in PIR format. Modeller provides two different methods to calculate pairwise sequence alignments. alignment.malign()
uses classical dynamic programming to align two sequences. alignment.alig2dn()
also uses a dynamic programming approach, but includes structural information to optimize the alignment (e.g. tries to place gaps outside of secondary structure elements). We applied both alignment methods and created eight pairwise sequnece alignments of the above templates with the target. The script used for this purpose is shown below:
from modeller import *
env = environ()
aln = alignment(env)
mdl = model(env, file='template_name', model_segment=('FIRST:@', 'END:'))
aln.append_model(mdl, align_codes='template_name', atom_files='template_name')
aln.append(file='1AUK.pir', align_codes='target_name')
aln.align2d()
aln.check()
aln.write(file='target-template-2d.ali', alignment_format='PIR')
aln.malign()
aln.check()
aln.write(file='target-template.ali', alignment_format='PIR')
For these alignments we constructed eight models, using the following script:
from modeller import *
from modeller.automodel import *
log.verbose()
env = environ()
a = automodel(env,
alnfile = '1AUK-1FSU-2d.ali',
knowns = '1FSU',
sequence = '1AUK',
assess_methods=(assess.DOPE, assess.GA341))
a.starting_model= 1
a.ending_model = 1
a.make()
We modified the paths and filenames in the scripts such that it matched our proteins of interest.
Next, we calculated RMSD and TM scores of the models to get a first impression on how much the models deviate from the original structure. The results are depicted in the table below.
Further on, we visualised the models using pymol. We load both structures into the program and performed a structural alignment to superimpose and compare them visually. The pymol commands and the images are shown below:
align 1AUK, MODEL
hide all
show cartoon
# select color of modelled structure via graphical interface
ray
cmd.png("1AUK.1P49.png")
Alignment method | 1P49 | 2VQR | 1FSU | 3ED4 |
Classical Dynamic Programming |
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Dynamic Programming with structural information from the template |
3ED4
Alignment method | 3ED4A | 3ED4B | 3ED4C | 3ED4D |
Dynamic Programming with structural information from the template |