Difference between revisions of "Homology Modeling of ARS A"
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To create pairwise alignments with the Needleman-Wunsch algorithm, we installed the European Molecular Biology Open Software (EMBOSS). |
To create pairwise alignments with the Needleman-Wunsch algorithm, we installed the European Molecular Biology Open Software (EMBOSS). |
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| − | <code> |
+ | #<code> |
| − | sudo apt-get install emboss |
+ | #sudo apt-get install emboss |
| − | </code> |
+ | #</code> |
Then, we executed the ''needle'' program with the following commands: |
Then, we executed the ''needle'' program with the following commands: |
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A tutorial on the usage of ''needle'' can be found [http://helixweb.nih.gov/emboss/html/needle.html here]. |
A tutorial on the usage of ''needle'' can be found [http://helixweb.nih.gov/emboss/html/needle.html here]. |
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| + | |||
| + | We executed Modeller with the following commands: |
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| + | |||
| + | <code> |
||
| + | /apps/modeller9.9/bin/mod9.9 aln_append_model.py |
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| + | /apps/modeller9.9/bin/mod9.9 model-default.py |
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| + | </code> |
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| + | |||
| + | We modified the paths and filenames in the scripts ''aln_append_model.py'' and ''model-default.py'' such that it matched our proteins of interest. |
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Revision as of 15:53, 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 | 31.9% |
| 1FSU | 28.0% | Homo Sapiens | Arylsulfatase B | yes | 26.5% |
| 2VQR | 20.0% | Rhizobium leguminosarum | Sulfatase | no | 20.3% |
| 3ED4 | 32.0% | Escherichia coli | Arylsulfatase | yes | 27.7% |
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
Then, we executed the needle program with the following commands:
needle -gapopen 10 -gapextend 0.5 -outfile 1p49.needle 1AUK.fasta.txt 1P49.fasta.txt
needle -gapopen 10 -gapextend 0.5 -outfile 1fsu.needle 1AUK.fasta.txt 1FSU.fasta.txt
needle -gapopen 10 -gapextend 0.5 -outfile 2vqr.needle 1AUK.fasta.txt 2VQR.fasta.txt
needle -gapopen 10 -gapextend 0.5 -outfile 3ed4.needle 1AUK.fasta.txt 3ED4.fasta.txt
A tutorial on the usage of needle can be found here.
We executed Modeller with the following commands:
/apps/modeller9.9/bin/mod9.9 aln_append_model.py
/apps/modeller9.9/bin/mod9.9 model-default.py
We modified the paths and filenames in the scripts aln_append_model.py and model-default.py such that it matched our proteins of interest.
