Difference between revisions of "Glucocerebrosidase homology modelling"
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MODELLER is a method for comparative protein structure modelling by satisfaction of spatial restraints. |
MODELLER is a method for comparative protein structure modelling by satisfaction of spatial restraints. |
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| + | |||
| + | === Results === |
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| + | |||
| + | === Analysis === |
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The results of Modeller were retrieved according to the [[Workflow_homology_modelling_glucocerebrosidase| Detailed Workflow]] |
The results of Modeller were retrieved according to the [[Workflow_homology_modelling_glucocerebrosidase| Detailed Workflow]] |
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| − | + | == iTasser == |
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| + | |||
| − | === SWISS-MODEL === |
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| + | === Results === |
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| + | |||
| + | === Analysis === |
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| + | |||
| + | == SWISS-MODEL == |
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SWISS-MODEL workspace was published by Arnold et al. in 2005. <ref> Arnold K., Bordoli L., Kopp J., and Schwede T. (2006). The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics, 22,195-201.</ref> |
SWISS-MODEL workspace was published by Arnold et al. in 2005. <ref> Arnold K., Bordoli L., Kopp J., and Schwede T. (2006). The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics, 22,195-201.</ref> |
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| − | + | === Results === |
|
| + | |||
| + | Using the standard output alignment of ClustalW2, the workunit of Swiss-Model got aborted: too many unfruitful attempts to rebuild a loop were tried. This indicates, that the alignment is not good and that it has to be adjusted. |
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| + | |||
| + | === Analysis === |
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| + | |||
| − | Using the standard output alignment of ClustalW, the workunit of Swiss-Model got aborted: too many unfruitful attempts to rebuild a loop were tried. This indicates, that the alignment is not good and that it has to be adjusted. |
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== References == |
== References == |
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Revision as of 12:01, 11 June 2011
Contents
Homologous Structures
The 10 best results of the sequence search with HHSearch (as retrieved in Task 1) are listed in the table below.
| > 60% sequence identity | ||||
| PDB-ID | name | organism | identity | template |
| 2nt0 | Glucosylceramidase | Homo Sapiens | 99% | |
| > 40% sequence identity | ||||
| PDB-ID | name | organism | identity | template |
| > 0% sequence identity | ||||
| PDB-ID | name | organism | identity | template |
| 2wnw | SrfJ | Salmonella enterica subsp. enterica | 29% | x |
| 3clw | conserved exported protein | Bacteroides fragilis | 13% | |
| 3kl0 | Glucuronoxylan Xylanohydrolase | Bacillus subtilis | 18% | x |
| 1nof | xylanase | Erwinia chrysanthemi | 18% | |
| 2e4t | Endoglucanase | Clostridium thermocellum | 11% | x |
| 3ii1 | Cellulase | Uncultured bacterium | 15% | |
| 1qw9 | Arabinosidase | Geobacillus stearothermophilus | 13% | |
| 1ik2 | Endoglucanase | Clostridium acetobutylicum | 12 % | |
| 2c7f | alpha-L-Arabinofuranosidase | Clostridium thermocellum | 16% | |
MODELLER
MODELLER is a method for comparative protein structure modelling by satisfaction of spatial restraints.
Results
Analysis
The results of Modeller were retrieved according to the Detailed Workflow
iTasser
Results
Analysis
SWISS-MODEL
SWISS-MODEL workspace was published by Arnold et al. in 2005. <ref> Arnold K., Bordoli L., Kopp J., and Schwede T. (2006). The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics, 22,195-201.</ref>
Results
Using the standard output alignment of ClustalW2, the workunit of Swiss-Model got aborted: too many unfruitful attempts to rebuild a loop were tried. This indicates, that the alignment is not good and that it has to be adjusted.
Analysis
References
<references />
