Difference between revisions of "Homology Modelling GLA"
m (→SWISS-MODEL) |
(→iTasser) |
||
Line 43: | Line 43: | ||
==iTasser== |
==iTasser== |
||
+ | As the iTasser-server has very low capacities, only one job commitment at the same time was possible and one job took about 36 hours to run, we obtained a license for academic or non-profit use. It empowered us to download the standalone package of iTasser and we were able to run it locally. |
||
==SWISS-MODEL== |
==SWISS-MODEL== |
Revision as of 23:59, 11 June 2011
by Benjamin Drexler and Fabian Grandke
Calculation of Models
Available Homologous Structures
The HHpred search from Task1 output the following sequences(Top 10):
PDB-ID | Name | Probability | E-value | P-value | Identity |
---|---|---|---|---|---|
> 60% sequence identity | |||||
3hg3_A | Alpha-galactosidase A | 1.0 | 0 | 0 | 97% |
> 40% sequence identity | |||||
1ktb_A | Alpha-N-acetylgalactosaminidase | 1.0 | 0 | 0 | 53% |
< 40% sequence identity | |||||
1uas_A | Alpha-galactosidase | 1.0 | 0 | 0 | 39% |
3lrk_A | Alpha-galactosidase 1 | 1.0 | 0 | 0 | 32% |
3a5v_A | Alpha-galactosidase | 1.0 | 0 | 0 | 35% |
1szn_A | Alpha-galactosidase | 1.0 | 0 | 0 | 34% |
3a21_A | Putative secreted alpha-galactosidase | 1.0 | 0 | 0 | 34% |
3cc1_A | BH1870 protein | 1.0 | 0 | 0 | 26% |
3a24_A | Alpha-galactosidase | 1.0 | 0 | 0 | 14% |
1zy9_A | Alpha-galactosidase | 1.0 | 2.2E-37 | 8.8E-42 | 14% |
MODELLER
iTasser
As the iTasser-server has very low capacities, only one job commitment at the same time was possible and one job took about 36 hours to run, we obtained a license for academic or non-profit use. It empowered us to download the standalone package of iTasser and we were able to run it locally.
SWISS-MODEL
Following sequences have been selected:
3hg3_A | 1ktb_A | 3cc1_A | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Automated Mode | Aligned Mode | Automated Mode | Aligned Mode | Automated Mode | Aligned Mode | |||||||||
Identity | Z-score | Model | Z-score | Model | Identity | Z-score | Model | Z-score | Model | Identity | Z-score | Model | Z-score | Model |
97% | 0 | -0.415 | 53% | 0 | -2.261 | 26% | 0 | Error¹ | NA |
¹The sequences are to different to create a useful model from the alignment. In the automated mode the template itself has been used as model, what is useless, because the sequences have only 26% identity.
Aborting: too many unfruitful attempts to rebuild a loop.
This is likely to indicate a misalignment in this region
Use Swiss-PdbViewer to adjust your alignment in this
region and resubmit an optimise mode modelling request.
Evaluation of Models
MODELLER
Numeric Evaluation
Comparison to Experimental Structure
iTasser
Numeric Evaluation
Comparison to Experimental Structure
SWISS-MODEL
Numeric Evaluation
Comparison to Experimental Structure
References
<references />