Difference between revisions of "Glucocerebrosidase homology modelling"
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| 2c7f ||alpha-L-Arabinofuranosidase || Clostridium thermocellum || 16% || |
| 2c7f ||alpha-L-Arabinofuranosidase || Clostridium thermocellum || 16% || |
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| + | For the different homology searches, the sequence of 1OGS was used, instead of P04062, as it does not contain the signal peptide which is not present in the mature protein. |
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== MODELLER == |
== MODELLER == |
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Revision as of 12:50, 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% | |
For the different homology searches, the sequence of 1OGS was used, instead of P04062, as it does not contain the signal peptide which is not present in the mature protein.
MODELLER
MODELLER is a method for comparative protein structure modelling, provided by satisfaction of spatial restraints. In the simplest case, the most probable structure for a given sequence can be found based on its alignment with related structures. Additional to model building, MODELLER can perform several other tasks including fold assignment, pairwise/ multiple alignments of protein sequences, calculation of phylogenetic trees, and de novo modeling of loops in protein structures. The method was published by Sali and Blundell in 1993. <ref>A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.</ref>
Usage
- Website with tutorials and download information: http://salilab.org/modeller/
- Description of the steps applied in this analysis: Detailed Workflow
Results
Analysis
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 />
