Difference between revisions of "Glucocerebrosidase homology modelling"
From Bioinformatikpedia
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=== SWISS-MODEL === |
=== SWISS-MODEL === |
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| − | SWISS-MODEL workspace was published by Arnold et al. in 2005. |
+ | 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> |
''' Usage - Automated Mode ''' |
''' Usage - Automated Mode ''' |
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Revision as of 12:43, 7 June 2011
Contents
Homologous Structures
The 10 best results of the sequence search with HHSearch are listed in the table below.
| > 60% sequence identity | ||
| PDB-ID | name | identity |
| 2nt0 | acid beta-glucosidase with pharmacological chaperone | 99% |
| > 40% sequence identity | ||
| PDB-ID | name | identity |
| > 0% sequence identity | ||
| PDB-ID | name | identity |
| 2wnw | Salmonella enterica serovar typhimurium virulence factor SrfJ | 29% |
| 3clw | conserved exported protein from Bacteroides fragilis | 14% |
| 1nof | xylanase | 18% |
| 3kl0 | Glucuronoxylan Xylanohydrolase | 20% |
| 3qw9 | betaglycan zona pellucida (ZP)-C domain | 15% |
| 2vrq | complex between a branched pentasaccharide and Thermobacillus xylanilyticus GH-51 arabinofuranosidase | 14% |
| 1uhv | beta-D-xylosidase from Thermoanaerobacterium saccharolyticum | 13% |
| 2c7f | family 51 arabinofuranosidase, Araf51, from Clostridium thermocellum | 15% |
| 3ii1 | bifunctional glucanase-xylanase CelM2 | 15% |
Calculation of Models
MODELLER
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>
Usage - Automated Mode
- Webserver: http://swissmodel.expasy.org/workspace/index.php?func=modelling_simple1
- Input: Sequence in fasta format
Usage - Alignment Mode
- Webserver: http://swissmodel.expasy.org/workspace/index.php?func=modelling_align1
- Input: Target-Template Alignment in different formats (FASTA, CLUSTALW, ...)
References
<references />
