Difference between revisions of "Gaucher Disease: Task 05 - Homology Modelling"

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(Structures from task 04)
(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
 
* > 60% sequence identity to our template protein, P04062 (536 aa)
 
* > 60% sequence identity to our template protein, P04062 (536 aa)
* < 30% sequence identity (ide ally go towards 20%)
+
* < 30% sequence identity
 
We calculated PID as follows:
 
We calculated PID as follows:
 
* 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]
 
* 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
Selected structures for modelling are written in bold.
+
Selected structures for modeling are written in bold.
   
 
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Revision as of 22:09, 10 June 2013

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

Modeller

SWISS-MODEL

I-TASSER

Evaluation of models