Difference between revisions of "Homology Modeling of ARS A"
From Bioinformatikpedia
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| − | == Proteins used as templates == |
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| + | == HHpred == |
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| + | We used the [http://toolkit.lmb.uni-muenchen.de/hhpred webserver] and |
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| + | == Modeller == |
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| + | === Proteins used as templates === |
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We identified the following proteins (see [[metachromatic_leukodystrophy_reference_aminoacids|Alignment TASK]]) as potential targets for homology modeling:used the following |
We identified the following proteins (see [[metachromatic_leukodystrophy_reference_aminoacids|Alignment TASK]]) as potential targets for homology modeling:used the following |
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Our potential tmeplates, identified by the database searches contain all homologs with known structure, regarding to HSSP. |
Our potential tmeplates, identified by the database searches contain all homologs with known structure, regarding to HSSP. |
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| − | == Modeller == |
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=== Pairwise alignments === |
=== Pairwise alignments === |
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Revision as of 12:38, 7 June 2011
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 | ? |
| 1FSU | 28.0% | Homo Sapiens | Arylsulfatase B | yes | 26.5% |
| 2VQR | 20.0% | Rhizobium leguminosarum | Sulfatase | no | ? |
| 3ED4 | 32.0% | Escherichia coli | Arylsulfatase | yes | ? |
Our potential tmeplates, identified by the database searches contain all homologs with known structure, regarding to HSSP.
Pairwise alignments
The programs used for TASK 2 are heuristics, which produce local alignments. If we call modeller with only one template structure, we need to globally align the seqeunces. To create pairwise alignments with the Needleman-Wunsch algorithm, we downloaded and installed EMBOSS.
wget ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-latest.tar.gz
tar -xzf EMBOSS-latest.tar.gz
cd EMBOSS-6.3.1/
./configure
sudo make
sudo make install
