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

From Bioinformatikpedia
(Structures from task 04)
(Structures from task 04)
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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]
 
* 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.
   
 
{| border="1" cellpadding="5" cellspacing="0" align="center"
 
{| border="1" cellpadding="5" cellspacing="0" align="center"
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! style="background:#efefef;" | < 30% PID
 
! style="background:#efefef;" | < 30% PID
 
|-
 
|-
|2xwd_A (82.77%) || 2f7k_A (9.65%)
+
|'''2xwd_A (82.77%)''' || 2f7k_A (9.65%)
 
|-
 
|-
|2nsx_A || 2gep_A (9.66%)
+
|2nsx_A || '''2gep_A (9.66%)'''
 
|-
 
|-
 
|2nt1_A || 2isb_A (7.17%)
 
|2nt1_A || 2isb_A (7.17%)
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|-
 
|-
 
|}
 
|}
 
   
 
==Evaluation of models==
 
==Evaluation of models==

Revision as of 00:06, 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
  • < 30% sequence identity (ideally go towards 20%)

For not glucocerebrosidases, 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 modelling are written in bold.

Homologous structures to 1ogs_A
> 60% PID < 30% PID
2xwd_A (82.77%) 2f7k_A (9.65%)
2nsx_A 2gep_A (9.66%)
2nt1_A 2isb_A (7.17%)
2djf_B (5.68%)
2qgu (7.17%)

Evaluation of models