Difference between revisions of "Homology Modeling of ARS A"

From Bioinformatikpedia
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== HHpred ==
 
== HHpred ==
   
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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.
 
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.
+
To create pairwise alignments with the Needleman-Wunsch algorithm, we installed the European Molecular Biology Open Software (EMBOSS).
   
 
<code>
 
<code>
  +
sudo apt-get install emboss
wget ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-latest.tar.gz <br>
 
tar -xzf EMBOSS-latest.tar.gz <br>
 
cd EMBOSS-6.3.1/ <br>
 
./configure <br>
 
sudo make <br>
 
sudo make install <br>
 
 
</code>
 
</code>

Revision as of 12:45, 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 installed the European Molecular Biology Open Software (EMBOSS).

sudo apt-get install emboss