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

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(Calculation of models)
(Modeller multiple target modeling)
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===Modeller multiple target modeling===
 
===Modeller multiple target modeling===
  +
In multiple target modeling Modeller first aligns the user selected templates, then adds the target to the MSA, which is finally used for modeling. We tried the following template combinations:
several close homologues (> 60% sequence identity): 2xwd_A and 2nsx_A
 
several distant homologues (< 30% sequence identity): TODO (we had only very distant structures in our set)
+
*several close homologues (> 60% sequence identity): 2xwd_A and 2nsx_A
  +
*several distant homologues (< 30% sequence identity): TODO (we had only very distant structures in our set)
one or more close and one or more distant homologues: TODO
 
  +
*one or more close and one or more distant homologues: TODO
   
 
==Evaluation of models==
 
==Evaluation of models==

Revision as of 23:07, 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 multiple target modeling

In multiple target modeling Modeller first aligns the user selected templates, then adds the target to the MSA, which is finally used for modeling. We tried the following template combinations:

  • several close homologues (> 60% sequence identity): 2xwd_A and 2nsx_A
  • several distant homologues (< 30% sequence identity): TODO (we had only very distant structures in our set)
  • one or more close and one or more distant homologues: TODO

Evaluation of models

Modeller

SWISS-MODEL

I-TASSER