Difference between revisions of "Glucocerebrosidase homology modelling"
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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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| − | ''' Usage - Automated Mode ''' |
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| − | * Webserver: http://swissmodel.expasy.org/workspace/index.php?func=modelling_simple1 |
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| − | * Input: Sequence in fasta format |
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| − | |||
| − | The automated mode should only be used, if target and template share more than 50% of sequence identity. This is not the case for the proteins selected as target in this case. Therefore the Alignment Mode will be used to create the models for glucocerebrosidase. |
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| − | |||
| − | ''' Usage - Alignment Mode ''' |
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| − | * Webserver: http://swissmodel.expasy.org/workspace/index.php?func=modelling_align1 |
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| − | * Input: Target-Template Alignment in different formats (FASTA, CLUSTALW, ...) |
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| − | To create the Alignments needed as input, the tool ClustalW was used. |
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==== 2WNW ==== |
==== 2WNW ==== |
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Revision as of 12:00, 11 June 2011
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.
The results of Modeller were retrieved according to the Detailed Workflow
iTasser
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>
2WNW
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.
References
<references />
