Difference between revisions of "Gaucher Disease: Task 05 - Homology Modelling"
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Kalemanovm (talk | contribs) (→Calculation of models) |
Kalemanovm (talk | contribs) (→Modeller multiple target modeling) |
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===Modeller multiple target modeling=== |
===Modeller multiple target modeling=== |
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+ | 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: |
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− | several close homologues (> 60% sequence identity): 2xwd_A and 2nsx_A |
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− | several |
+ | *several close homologues (> 60% sequence identity): 2xwd_A and 2nsx_A |
+ | *several distant homologues (< 30% sequence identity): TODO (we had only very distant structures in our set) |
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− | one or more close and one or more distant homologues: TODO |
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+ | *one or more close and one or more distant homologues: TODO |
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==Evaluation of models== |
==Evaluation of models== |
Revision as of 23:07, 10 June 2013
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 PID using SIAS with default options
Selected structures for modeling 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 |
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): TODO (we had only very distant structures in our set)
- one or more close and one or more distant homologues: TODO