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

From Bioinformatikpedia
(Evaluation of models)
(Modeller)
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===Modeller===
 
===Modeller===
[[File:P04062-mixed-model.png|Model using templates with mixed sequence identity: high '''2XWD''' and low '''2WNW''' and '''salign''' alignment method.]]
 
   
 
<gallery widths=225px heights=200px caption="Pymol alignment of models of P04062 computed by Modeller (lime) with the original structure 1OGS, chain A (purple).">
 
<gallery widths=225px heights=200px caption="Pymol alignment of models of P04062 computed by Modeller (lime) with the original structure 1OGS, chain A (purple).">
File:P04062-2XWD-malign-model.png|Model using template '''2XWD''' and '''malign''' alignment method.
+
File:P04062-2XWD-malign-model.png|Model using template '''2XWD''' and '''malign''' alignment method. RMSD(C_alpha) = 0.284 (408 aligned atoms).
File:P04062-2XWD-salign-model.png|Model using template '''2XWD''' and '''salign''' alignment method.
+
File:P04062-2XWD-salign-model.png|Model using template '''2XWD''' and '''salign''' alignment method. RMSD(C_alpha) = 0.284 (408 aligned atoms).
File:P04062-2WNW-malign-model.png|Model using template '''2WNW''' and '''malign''' alignment method.
+
File:P04062-2WNW-malign-model.png|Model using template '''2WNW''' and '''malign''' alignment method. RMSD(C_alpha) = 1.217 (340 aligned atoms).
File:P04062-2WNW-salign-model.png|Model using template '''2WNW''' and '''salign''' alignment method.
+
File:P04062-2WNW-salign-model.png|Model using template '''2WNW''' and '''salign''' alignment method. RMSD(C_alpha) = 1.523 (337 aligned atoms).
 
File:P04062-high-model.png|Model using templates with high sequence identity: '''3KE0''', '''2XWD''', '''2WKL''' and '''2NSX''' and '''salign''' alignment method. RMSD(C_alpha)= 0.272 (439 aligned atoms).
 
File:P04062-high-model.png|Model using templates with high sequence identity: '''3KE0''', '''2XWD''', '''2WKL''' and '''2NSX''' and '''salign''' alignment method. RMSD(C_alpha)= 0.272 (439 aligned atoms).
 
File:P04062-low-model.png|Model using templates with high sequence identity: '''2WNW''', '''1VFF''' and '''3II1''' and '''salign''' alignment method. RMSD(C_alpha) = 20.935 (471 aligned atoms).
 
File:P04062-low-model.png|Model using templates with high sequence identity: '''2WNW''', '''1VFF''' and '''3II1''' and '''salign''' alignment method. RMSD(C_alpha) = 20.935 (471 aligned atoms).
File:P04062-mixed-model.png|Model using templates with mixed sequence identity: high '''2XWD''' and low '''2WNW''' and '''salign''' alignment method. RMSD(C_alpha) = 0.328 (418 aligned atoms)
+
File:P04062-mixed-model.png|Model using templates with mixed sequence identity: high '''2XWD''' and low '''2WNW''' and '''salign''' alignment method. RMSD(C_alpha) = 0.328 (418 aligned atoms).
 
</gallery>
 
</gallery>
   

Revision as of 01:45, 22 August 2013

This page is still under construction.

Calculation of models

Lab journal

Modeller

We created two single target models of our protein sequence, P04062: one with a high sequence identity target,'2XWD_A, and one with a low sequence identity target, 2WNW_A. 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:

  • close homologues (> 60% sequence identity): all four (3KE0_A, 2XWD_A, 2WKL_A and 2NSX_A)
  • distant homologues (< 30% sequence identity): all three (2WNW_A, 1VFF_A and 3II1_A)
  • close and distant homologues: 2XWD_A and 2WNW_A

Swissmodel

Model for 2GEP could not be created, because the alignment quality between target and specified template (2GEP) is too low and they could not be aligned with BLAST or HHsearch.

iTasser

The run with 2XWD as template is still running on the server.

For details how we executed the programs please see the lab journal.

Evaluation of models

Modeller

Swissmodel

iTasser