Difference between revisions of "Homology Modeling of ARS A"
From Bioinformatikpedia
| Line 36: | Line 36: | ||
sudo make <br> |
sudo make <br> |
||
sudo make install <br> |
sudo make install <br> |
||
| − | < |
+ | </code> |
Revision as of 12:31, 7 June 2011
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.
Modeller
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
