Difference between revisions of "Homology Modelling GLA"
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==iTasser== |
==iTasser== |
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+ | Figure 2 shows, that iTasser takes an amino acid sequence as input and tries to retrieve template proteins from PDB. In the next step fragments from the the templates are reassembled to a complete model. In the last step, the model is reassembled by taking energy calculations into account. Additionally biological function prediction is done, but that was not of interest of this task.<ref name=itasser1>[http://zhanglab.ccmb.med.umich.edu/I-TASSER/about.html]</ref> |
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− | 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(takes another 36h). It empowered us to download the standalone package of iTasser. Unfortunately, it is about 8gb big and does not work properly! Thus we still used the server with different IP- and e-mail addresses. |
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+ | [[File:GLA_Itasser.png|200px|thumb|right| Figure 1: A schematic representation of the I-TASSER protocol for protein structure and function predictions. The protein chains are colored from blue at the N-terminus to red at the C-terminus.<ref name=itasser2>Roy et al., I-TASSER: a unified platform for automated protein structure and function prediction, Nature Protocols, 2007</ref>]] |
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+ | <!--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(takes another 36h). It empowered us to download the standalone package of iTasser. Unfortunately, it is about 8gb big and does not work properly! Thus we still used the server with different IP- and e-mail addresses.--> |
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==SWISS-MODEL== |
==SWISS-MODEL== |
Revision as of 20:01, 13 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
Figure 2 shows, that iTasser takes an amino acid sequence as input and tries to retrieve template proteins from PDB. In the next step fragments from the the templates are reassembled to a complete model. In the last step, the model is reassembled by taking energy calculations into account. Additionally biological function prediction is done, but that was not of interest of this task.<ref name=itasser1>[1]</ref>
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 />