Difference between revisions of "Homology Modelling GLA"

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==iTasser==
 
==iTasser==
Figure 1 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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Figure 1 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>
 
[[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>]]
 
[[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>]]
   

Revision as of 21:16, 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 1 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>

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>


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 />