Difference between revisions of "Gaucher Disease: Task 05 - Homology Modelling"
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Kalemanovm (talk | contribs) (→Structures from task 04) |
Kalemanovm (talk | contribs) (→Structures from task 04) |
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We assembled the following structures in [[Gaucher_Disease:_Task_04_-_Structural_Alignment]], now we divide them into two groups at |
We assembled the following structures in [[Gaucher_Disease:_Task_04_-_Structural_Alignment]], now we divide them into two groups at |
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* > 60% sequence identity to our template protein, P04062 (536 aa) |
* > 60% sequence identity to our template protein, P04062 (536 aa) |
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− | * < 30% sequence identity |
+ | * < 30% sequence identity |
We calculated PID as follows: |
We calculated PID as follows: |
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* first aligned the two fasta sequences from PDB with [http://www.genome.jp/tools-bin/clustalw ClustalW] |
* first aligned the two fasta sequences from PDB with [http://www.genome.jp/tools-bin/clustalw ClustalW] |
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* then calculated the PID using [http://imed.med.ucm.es/cgi-bin/sias.cgi?jobid=1370816376 SIAS] with default options |
* then calculated the PID using [http://imed.med.ucm.es/cgi-bin/sias.cgi?jobid=1370816376 SIAS] with default options |
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− | Selected structures for |
+ | Selected structures for modeling are written in bold. |
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Revision as of 22:09, 10 June 2013
Contents
Calculation of models
Structures from task 04
We assembled the following structures in Gaucher_Disease:_Task_04_-_Structural_Alignment, now we divide them into two groups at
- > 60% sequence identity to our template protein, P04062 (536 aa)
- < 30% sequence identity
We calculated PID as follows:
- first aligned the two fasta sequences from PDB with ClustalW
- then calculated the PID using SIAS with default options
Selected structures for modeling are written in bold.
Homologous structures to 1ogs_A | ||
---|---|---|
Structure | PID with target | Length |
2xwd_A | 91.51% | 505 aa |
2nsx_A | 92.53% | 497 aa |
2nt1_A | 92.53% | 497 aa |
2gep_A | 10.74% | 497 aa |
2f7k_A | 8.95% | 327 aa |
2qgu | 5.59% | 211 aa |
2isb_A | 5.59% | 192 aa |
2djf_A | 3.17% | 119 aa |
2djf_B | 2.98% | 164 aa |
2djf_C | 4.47% | 69 aa |