Difference between revisions of "Homology Modeling of ARS A"

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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