Homology Modelling GLA

From Bioinformatikpedia
Revision as of 22:59, 11 June 2011 by Grandke (talk | contribs) (iTasser)

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 />