Difference between revisions of "Glucocerebrosidase homology modelling"
(→MODELLER) |
(→MODELLER) |
||
| Line 41: | Line 41: | ||
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> |
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/ |
||
| + | * [[Workflow_homology_modelling_glucocerebrosidase| Detailed Workflow]] (Description of the steps applied in this analysis) |
||
=== Results === |
=== Results === |
||
=== Analysis === |
=== Analysis === |
||
| − | |||
| − | The results of Modeller were retrieved according to the [[Workflow_homology_modelling_glucocerebrosidase| Detailed Workflow]] |
||
== iTasser == |
== iTasser == |
||
Revision as of 12:20, 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, 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/
- Detailed Workflow (Description of the steps applied in this analysis)
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 />
