Difference between revisions of "Homology Modelling GLA"
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− | | 3LX9_A || style="background: #9ACD32;"| || style="background: #9ACD32;" | || 99%|| |
+ | | [http://www.pdb.org/pdb/explore/explore.do?structureId=3LX9 3LX9_A] || style="background: #9ACD32;"| || style="background: #9ACD32;" | || 99%|| |
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− | | 3GXP_A || style="background: #9ACD32;"| || style="background: #9ACD32;" | || 99%|| |
+ | | [http://www.pdb.org/pdb/explore/explore.do?structureId=3GXP 3GXP_A] || style="background: #9ACD32;"| || style="background: #9ACD32;" | || 99%|| |
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− | | 3H53_A || style="background: #9ACD32;"| || style="background: #9ACD32;" | || 99%|| |
+ | | [http://www.pdb.org/pdb/explore/explore.do?structureId=3H53 3H53_A] || style="background: #9ACD32;"| || style="background: #9ACD32;" | || 99%|| |
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− | | 3HG3_A || style="background: #9ACD32;"| || style="background: #9ACD32;" | || 97%|| |
+ | | [http://www.pdb.org/pdb/explore/explore.do?structureId=3HG3 3HG3_A] || style="background: #9ACD32;"| || style="background: #9ACD32;" | || 97%|| |
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− | | 3IGU_A || style="background: #9ACD32;"| || style="background: #9ACD32;" | || 54%|| |
+ | | [http://www.pdb.org/pdb/explore/explore.do?structureId=3IGU 3IGU_A] || style="background: #9ACD32;"| || style="background: #9ACD32;" | || 54%|| |
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− | | 1KTB_A || style="background: #9ACD32;"| || style="background: #9ACD32;" | || 53% || |
+ | | [http://www.pdb.org/pdb/explore/explore.do?structureId=1KTB 1KTB_A] || style="background: #9ACD32;"| || style="background: #9ACD32;" | || 53% || |
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− | | 1UAS_A || style="background: #9ACD32;"| || style="background: #9ACD32;" | || 39%|| |
+ | | [http://www.pdb.org/pdb/explore/explore.do?structureId=1UAS 1UAS_A] || style="background: #9ACD32;"| || style="background: #9ACD32;" | || 39%|| |
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− | | 3LRK_A || style="background: #9ACD32;"| || style="background: #FF4500;" | || 34% ||Was removed due to little sequence identity. Caused huge gaps in alignment. |
+ | | [http://www.pdb.org/pdb/explore/explore.do?structureId=3LRK 3LRK_A] || style="background: #9ACD32;"| || style="background: #FF4500;" | || 34% ||Was removed due to little sequence identity. Caused huge gaps in alignment. |
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− | | 3CC1_A || style="background: #9ACD32;"| || style="background: #FF4500;" | || 28% ||Was removed due to little sequence identity. Caused huge gaps in alignment. |
+ | | [http://www.pdb.org/pdb/explore/explore.do?structureId=3CC1 3CC1_A] || style="background: #9ACD32;"| || style="background: #FF4500;" | || 28% ||Was removed due to little sequence identity. Caused huge gaps in alignment. |
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Revision as of 02:49, 14 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
We used the MODELLER as described in the tutorial Using Modeller for TASK 4.
PDB-ID | Unsupervised | Supervised | Identity | Comment |
---|---|---|---|---|
3LX9_A | 99% | |||
3GXP_A | 99% | |||
3H53_A | 99% | |||
3HG3_A | 97% | |||
3IGU_A | 54% | |||
1KTB_A | 53% | |||
1UAS_A | 39% | |||
3LRK_A | 34% | Was removed due to little sequence identity. Caused huge gaps in alignment. | ||
3CC1_A | 28% | Was removed due to little sequence identity. Caused huge gaps in alignment. |
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>
![](/wiki/images/thumb/0/08/GLA_Itasser.png/200px-GLA_Itasser.png)
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 />