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 ===
 
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.
 
== Modeller ==
 
 
 
=== Pairwise alignments ===
 
=== Pairwise alignments ===
   

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