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

From Bioinformatikpedia
(Structures from task 04)
(Structures from task 04)
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! style="background:#efefef;" | Structure
 
! style="background:#efefef;" | Structure
! style="background:#efefef;" | PID
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! style="background:#efefef;" | PID with target
! style="background:#efefef;" | Alignment length
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! style="background:#efefef;" | Length
 
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!2xwd_A || 91.51% || align="center"| 505 aa
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!2xwd_A || 91.51% || 505 aa
 
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|align="center"| 2nsx_A || align="center"| 92.53% || align="center"| 497 aa
 
|align="center"| 2nsx_A || align="center"| 92.53% || align="center"| 497 aa
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|align="center"| 2f7k_A || align="center"| 8.95% || align="center"| 327 aa
 
|align="center"| 2f7k_A || align="center"| 8.95% || align="center"| 327 aa
 
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!2gep_A || || align="center"| 497 aa
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!2gep_A || 10.74% || 497 aa
 
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|align="center"| 2isb_A || align="center"| 5.59% || align="center"| 192 aa
 
|align="center"| 2isb_A || align="center"| 5.59% || align="center"| 192 aa
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|align="center"| 2djf_C || align="center"| 4.47% || align="center"| 69 aa
 
|align="center"| 2djf_C || align="center"| 4.47% || align="center"| 69 aa
 
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|align="center"| 2qgu || align="center"| || align="center"|
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|align="center"| 2qgu || align="center"| 5.59% || align="center"| 211 aa
 
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Revision as of 22:07, 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 (ide ally go towards 20%)

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
Structure PID with target Length
2xwd_A 91.51% 505 aa
2nsx_A 92.53% 497 aa
2nt1_A 92.53% 497 aa
2f7k_A 8.95% 327 aa
2gep_A 10.74% 497 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
2qgu 5.59% 211 aa

Modeller

SWISS-MODEL

I-TASSER

Evaluation of models