Gaucher Disease: Task 05 - Homology Modelling
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Contents
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 PIDE (pairwise sequence identity) using SIAS with default options
Selected structures for modeling are written in bold.
Homologous structures to 1ogs_A | ||
---|---|---|
Structure | PIDE with target | Length |
High PIDE | ||
2xwd_A | 91.51% | 505 aa |
2nsx_A | 92.53% | 497 aa |
2nt1_A | 92.53% | 497 aa |
Low PIDE | ||
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): DODO (we had only very distant structures in our set)
- one or more close and one or more distant homologues: TODO
Swiss-Model
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.
I-TASSER
The run with 2xwd as template is still running on the server.
Evaluation of models
Modeller
Swiss-Model