Difference between revisions of "Gaucher Disease: Task 05 - Lab Journal"

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'''This page is still under construction'''
  
'''This page is still under construction'''
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==Calculation of models==
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  +
===Structures set===
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We assembled the following structures in [[Gaucher_Disease:_Task_04_-_Structural_Alignment|task 4]], now we divide them into two groups: at > 60% and at < 30% sequence identity to our template protein, P04062 (536 aa long).
  +
PIDE was calculated as follows:
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* first we aligned the two fasta sequences from PDB with [http://www.genome.jp/tools-bin/clustalw ClustalW]
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* then calculated the PIDE (pairwise sequence identity) using [http://imed.med.ucm.es/cgi-bin/sias.cgi?jobid=1370816376 SIAS] with default options
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Selected structures for single-template modelling are written in bold.
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{| border="1" cellpadding="5" cellspacing="0" align="center"
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|-
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!colspan="3" style="background:#adceff;" | Homologous structures to P04062
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|-
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! style="background:#efefef;" | PDB ID
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! style="background:#efefef;" | PIDE with target (%)
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! style="background:#efefef;" | Length (aa)
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|-
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!colspan="3" | High PIDE
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|-
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!2XWD_A || 91.51 || 505
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|-
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|align="center"| 2NSX_A || align="center"| 92.53 || align="center"| 497
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|-
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|align="center"| 2NT1_A || align="center"| 92.53 || align="center"| 497
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|-
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!colspan="3" | Low PIDE
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|-
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!2GEP_A || 10.74 || 497
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|-
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|align="center"| 2F7K_A || align="center"| 8.95 || align="center"| 327
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|-
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|align="center"| 2QGU || align="center"| 5.59 || align="center"| 211
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|-
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|align="center"| 2ISB_A || align="center"| 5.59 || align="center"| 192
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|-
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|align="center"| 2DJF_A || align="center"| 3.17 || align="center"| 119
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|-
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|align="center"| 2DJF_B || align="center"| 2.98 || align="center"| 164
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|-
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|align="center"| 2DJF_C || align="center"| 4.47 || align="center"| 69
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|-
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|}
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As the PIDE with P04062 in the low-PIDE group we have selected in task 4 is too low and 10.74% PIDE with 2GEP_A was not enough for Swissmodel to align the sequences, we looked again at the found hit list in [[Gaucher Disease: Task 02 - Alignments|task 2]] (HHblits, 2 iterations against Uniprot20 followed by one iteration against pdb_full with E-value cutoff 10E-10). The set of structures finally used is:
  +
  +
{| border="1" cellpadding="5" cellspacing="0" align="center"
  +
|-
  +
!colspan="5" style="background:#adceff;" | Homologous structures to P04062
  +
|-
  +
! style="background:#efefef;" | PDB ID
  +
! style="background:#efefef;" | PIDE of alignment with target (%)
  +
! style="background:#efefef;" | Length (aa)
  +
! style="background:#efefef;" | Aligned columns (aa)
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! style="background:#efefef;" | Query coverage
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|-
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!colspan="5" | High PIDE
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|-
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|align="center"| 3KE0_A || align="center"| 100 || align="center"| 497 || align="center"| 496 || align="center"| 41-536
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|-
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!align="center"| 2XWD_A || align="center"| 100 || align="center"| 505 || align="center"| 497 || align="center"| 40-536
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|-
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|align="center"| 2WKL_A || align="center"| 100 || align="center"| 497 || align="center"| 496 || align="center"| 41-536
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|-
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|align="center"| 2NSX_A || align="center"| 100 || align="center"| 497 || align="center"| 496 || align="center"| 41-536
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|-
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!colspan="5" | Low PIDE
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|-
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!align="center"| 2WNW_A || align="center"| 29 || align="center"| 447 || align="center"| 440 || align="center"| 75-534
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|-
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|align="center"| 1VFF_A || align="center"| 22 || align="center"| 423 || align="center"| 98 || align="center"| 151-228
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|-
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|align="center"| 3II1_A || align="center"| 20 || align="center"| 535 || align="center"| 84 || align="center"| 452-514
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|-
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|}
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===Modeller===
  
===Modeller===
   

Revision as of 01:09, 22 August 2013

This page is still under construction

Calculation of models

Structures set

We assembled the following structures in task 4, now we divide them into two groups: at > 60% and at < 30% sequence identity to our template protein, P04062 (536 aa long). PIDE was calculated as follows:

  • first we aligned the two fasta sequences from PDB with ClustalW
  • then calculated the PIDE (pairwise sequence identity) using SIAS with default options

Selected structures for single-template modelling are written in bold.

Homologous structures to P04062
PDB ID PIDE with target (%) Length (aa)
High PIDE
2XWD_A 91.51 505
2NSX_A 92.53 497
2NT1_A 92.53 497
Low PIDE
2GEP_A 10.74 497
2F7K_A 8.95 327
2QGU 5.59 211
2ISB_A 5.59 192
2DJF_A 3.17 119
2DJF_B 2.98 164
2DJF_C 4.47 69

As the PIDE with P04062 in the low-PIDE group we have selected in task 4 is too low and 10.74% PIDE with 2GEP_A was not enough for Swissmodel to align the sequences, we looked again at the found hit list in task 2 (HHblits, 2 iterations against Uniprot20 followed by one iteration against pdb_full with E-value cutoff 10E-10). The set of structures finally used is:

Homologous structures to P04062
PDB ID PIDE of alignment with target (%) Length (aa) Aligned columns (aa) Query coverage
High PIDE
3KE0_A 100 497 496 41-536
2XWD_A 100 505 497 40-536
2WKL_A 100 497 496 41-536
2NSX_A 100 497 496 41-536
Low PIDE
2WNW_A 29 447 440 75-534
1VFF_A 22 423 98 151-228
3II1_A 20 535 84 452-514

Modeller

Swissmodel

iTasser

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