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

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===Swiss-Model===
 
===Swiss-Model===
[[File:P04062-2WNW-model.png|Model using template '''2WNW'''. RMSD=1.105 (368 C_alpha atoms pairs).]]
 
   
 
<gallery widths=225px heights=150px caption="Pymol alignment of models of P04062 computed by Swiss-Model (lime) with the original structure 1OGS, chain A (purple). For the templates, chains A were used.">
 
<gallery widths=225px heights=150px caption="Pymol alignment of models of P04062 computed by Swiss-Model (lime) with the original structure 1OGS, chain A (purple). For the templates, chains A were used.">

Revision as of 11:47, 23 August 2013

This page is still under construction.

Calculation of models

Lab journal

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, with each one of the three tools: Modeller, Swiss-Model and iTasser.

For Modeller we additionally executed multiple target modeling mode. In the multiple target modeling mode, 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

Evaluation of models

Modeller

Swiss-Model

iTasser