Difference between revisions of "Homology-modelling HEXA"

From Bioinformatikpedia
(RMSD)
(RMSD and TM-Score)
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|[[Image:tm_superpose_itasser_model4_3bc9.png|thumb|150px|Superposition by TM-align with the structure predicted by iTasser (Model 4)]]
 
|[[Image:tm_superpose_itasser_model4_3bc9.png|thumb|150px|Superposition by TM-align with the structure predicted by iTasser (Model 4)]]
 
|[[Image:tm_superpose_itasser_model5_3bc9.png|thumb|150px|Superposition by TM-align with the structure predicted by iTasser (Model 5)]]
 
|[[Image:tm_superpose_itasser_model5_3bc9.png|thumb|150px|Superposition by TM-align with the structure predicted by iTasser (Model 5)]]
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|already running
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|-
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|}
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<br><br>
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''' Results for 3CUI:'''
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{| border="1" style="text-align:center; border-spacing:0;"
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|
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|Swissmodel
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|Modeller
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|iTasser Model 1
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|iTasser Model 2
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|-
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|RMSD (Pymol)
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|24.447
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|23.856
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|1.13
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|4.168
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|-
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|RMSD (TM-align)
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|5.49
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|5.46
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|0.56
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|3.73
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|-
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|TM Score
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|0.45333
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|0.44048
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|0.92583
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|0.75323
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|-
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|Structural alignment (Pymol)
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|[[Image:superpose_swissmodel_3cui.png|thumb|150px|Superposition by Pymol with the structure predicted by Modeller]]
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|[[Image:superpose_modeller_3cui.png|thumb|150px|Superposition by Pymol with the structure predicted by Modeller]]
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|[[Image:superpose_itasser_model1_3cui.png|thumb|150px|Superposition by Pymol with the structure predicted by iTasser (Model 1)]]
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|[[Image:superpose_itasser_model2_3cui.png|thumb|150px|Superposition by Pymol with the structure predicted by iTasser (Model 2)]]
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|-
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|Structural alignment (TM-align)
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|[[Image:tm_superpose_swissmodel_3cui.png|thumb|150px|Superposition by TM-align with the structure predicted by Modeller]]
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|[[Image:tm_superpose_modeller_3cui.png|thumb|150px|Superposition by TM-align with the structure predicted by Modeller]]
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|[[Image:tm_superpose_itasser_model1_3cui.png|thumb|150px|Superposition by TM-align with the structure predicted by iTasser (Model 1)]]
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|[[Image:tm_superpose_itasser_model2_3cui.png|thumb|150px|Superposition by TM-align with the structure predicted by iTasser (Model 2)]]
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|colspan="5" |
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|-
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|
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|iTasser Model 3
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|iTasser Model 4
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|iTasser Model 5
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|Jigsaw
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|-
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|RMSD (Pymol)
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|8.979
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|1.443
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|16.502
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|already running
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|-
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|RMSD (TM-align)
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|4.72
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|1.26
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|5.86
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|already running
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|-
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|TM-Score
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|0.60810
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|0.91279
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|0.40638
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|already running
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|-
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|Structural alignment (Pymol)
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|[[Image:superpose_itasser_model3_3cui.png|thumb|150px|Superposition by Pymol with the structure predicted by iTasser (Model 3)]]
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|[[Image:superpose_itasser_model4_3cui.png|thumb|150px|Superposition by Pymol with the structure predicted by iTasser (Model 4)]]
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|[[Image:superpose_itasser_model5_3cui.png|thumb|150px|Superposition by Pymol with the structure predicted by iTasser (Model 5)]]
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|already running
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|-
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|Structural alignment (TM-align)
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|[[Image:tm_superpose_itasser_model3_3cui.png|thumb|150px|Superposition by TM-align with the structure predicted by iTasser (Model 3)]]
  +
|[[Image:tm_superpose_itasser_model4_3cui.png|thumb|150px|Superposition by TM-align with the structure predicted by iTasser (Model 4)]]
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|[[Image:tm_superpose_itasser_model5_3cui.png|thumb|150px|Superposition by TM-align with the structure predicted by iTasser (Model 5)]]
 
|already running
 
|already running
 
|-
 
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Revision as of 13:32, 13 June 2011

Homology structure groups

We decided to choose every 5% one protein:

> 60% sequence identity
PDB id name similarity single template
1ht6_A AMY1, alpha-amylase iso 95%
3aj7_A Oligo-1,6-glucosidase 90%
1h4p_A Glucan 1,3-beta-glucosidase 85.2%
3bc9_A AMYB, alpha amylase, ca 80.8% X
2zum_A 458AA long hypothetical 75%
3bmv_A Cyclomaltodextrin gluca 70.3%
2f2h_A Putative family 31 gluc 64.8%
3emz_A Xylanase, endo-1,4-beta 61%
> 40%
2dep_A Xylanase B, thermostabl 54.9%
3cui_A EXO-beta-1,4-glucanase; 49.5% X
1vhc_A Putative KHG/KDPG aldol 45.1%
2hk0_A D-psicose 3-epimerase 40.8%
< 40%
2g0w_A LMO2234 protein; putati 35.5%
3q94_A Fructose-bisphosphate a 30.0%
3hn3_A Beta-G1, beta-glucuroni 25.1%
3lut_A Voltage-gated potassium 20.1% X

Calculation of the models

Swissmodel

To calculate the models with Swiss-Model we used the [Webserver]. For the template with high sequence identity, we used the automated and the alignment method, for the other two templates we only used the alignment method.

The used alignments can be found [here].

Modeller

We used Modeller from the command line. Therefore we followed the instructions, described [here].

First of all, we created an alignment for each of our three selected sequences. In the next step we used Modeller to model the 3D structure of the protein.

For Modeller we used the Pir Alignment format, which can be found here: [3BC9], [3CUI], [3LUT]

iTasser

To calculate our models with iTasser we used the [Webserver]. We defined the target and template sequence, but this time without an alignment. We used the same template sequences as before.

Results

Swissmodel

3BC9:

todo

3CUI:

The detailed prediction can be found [here]

Swiss-Model also give same scores to give the user the possibility to estimate the quality of the predicted model, which are showed in the next paragraphes.

The most important score in the following table is the QMEAN4 score, because this score consists of the scores above and give the user the possibility to compare different results.

 Global Score
Scoring function term Raw score Z score
C_beta interaction energy 202.24 -4.65
All-atom pairwise energy 9942.28 -6.16
Solvation energy 67.79 -8.08
Torsion angle energy 76.36 -7.72
QMEAN4 score 0.057 -11.76

Swiss-Modeler also returns some pictures, which show the qualitity of the model.

Predicted Structure:

Prediction the structure of HEXA_HUMAN with 3cui as template structure
Prediction of the wrong predicted residues



Model qualitity:

Visualisation of the QMEAN Z-Score for this model
Visualisation of the QMEAN score in comparison with a gaussian distribution
Quality of the model in comparison to a X-ray structure
Plot, which shows the wrong predicted residues of this model


3HN3:

The detailed prediction can be found [here]

Swiss-Model also give same scores to give the user the possibility to estimate the quality of the predicted model, which are showed in the next paragraphes.

The most important score in the following table is the QMEAN4 score, because this score consists of the scores above and give the user the possibility to compare different results.

Global Score
Scoring function term Raw score Z score
C_beta interaction energy 120.70 -5.31
All-atom pairwise energy 2585.98 -5.22
Solvation energy 71.87 -9.92
Torsion angle energy 80.43 -8.44
QMEAN4 score 0.010 -12.80

Swiss-Modeler also returns some pictures, which show the qualitity of the model.

Predicted Structure:

Prediction the structure of HEXA_HUMAN with 3hn3 as template structure
Prediction of the wrong predicted residues



Model qualitity:

Visualisation of the QMEAN Z-Score for this model
Visualisation of the QMEAN score in comparison with a gaussian distribution
Quality of the model in comparison to a X-ray structure
Plot, which shows the wrong predicted residues of this model

Modeller

3BC9:

Modeller calculated one model for 3BC9, which can be seen in the next picture:

3D structure of HEXA_HUMAN with 3BC9 as template predicted by Modeller.

3CUI:

Modeller calculated one model for 3CUI, which can be seen in the next picture:

3D structure of HEXA_HUMAN with 3CUI as template predicted by Modeller.

3HN3:

TODO Dienstag

iTasser

Analysis

RMSD and TM-Score

To get the possibility to estimate the quality of the predicted models, we calculated the RMSD between the observed protein and the predicted protein. For this purpose, we used PyMol, because PyMol is able to superpose two 3D protein structures and to calculate the RMSD. Furthermore, we used TM-align to calculate the RMSD and also the TM-Score. Therefore, we used following command:

align model1, model2

As an output, we got the superposed structures, the number of aligned residues and the RMSD.

We decided not to use the RMSD, which is calculated by Modeller, because we wanted to calculate the RMSD for each structure in the same way, to get comparative results. In the pictures, which show the superposed structures, the green one is always the target, whereas the red one is always the template.

Results for 3BC9:

Swissmodel Modeller iTasser Model 1 iTasser Model 2
RMSD (Pymol) todo 26.271 1.075 16.450
RMSD (TM-align) todo 5.94 0.63 5.76
TM Score todo 0.43072 0.92545 0.41556
Structural alignment (Pymol) todo
Superposition by Pymol with the structure predicted by Modeller
Superposition by Pymol with the structure predicted by iTasser (Model 1)
Superposition by Pymol with the structure predicted by iTasser (Model 2)
Structural alignment (TM-align)
Superposition by TM-align with the structure predicted by Modeller
Superposition by TM-align with the structure predicted by iTasser (Model 1)
Superposition by TM-align with the structure predicted by iTasser (Model 2)
iTasser Model 3 iTasser Model 4 iTasser Model 5 Jigsaw
RMSD (Pymol) 19.716 10.824 20.450 already running
RMSD (TM-align) 5.54 6.27 5.55 already running
TM-Score 0.39710 0.50099 0.39822 already running
Structural alignment (Pymol)
Superposition by Pymol with the structure predicted by iTasser (Model 3)
Superposition by Pymol with the structure predicted by iTasser (Model 4)
Superposition by Pymol with the structure predicted by iTasser (Model 5)
already running
Structural alignment (TM-align)
Superposition by TM-align with the structure predicted by iTasser (Model 3)
Superposition by TM-align with the structure predicted by iTasser (Model 4)
Superposition by TM-align with the structure predicted by iTasser (Model 5)
already running



Results for 3CUI:

Swissmodel Modeller iTasser Model 1 iTasser Model 2
RMSD (Pymol) 24.447 23.856 1.13 4.168
RMSD (TM-align) 5.49 5.46 0.56 3.73
TM Score 0.45333 0.44048 0.92583 0.75323
Structural alignment (Pymol)
Superposition by Pymol with the structure predicted by Modeller
Superposition by Pymol with the structure predicted by Modeller
Superposition by Pymol with the structure predicted by iTasser (Model 1)
Superposition by Pymol with the structure predicted by iTasser (Model 2)
Structural alignment (TM-align)
Superposition by TM-align with the structure predicted by Modeller
Superposition by TM-align with the structure predicted by Modeller
Superposition by TM-align with the structure predicted by iTasser (Model 1)
Superposition by TM-align with the structure predicted by iTasser (Model 2)
iTasser Model 3 iTasser Model 4 iTasser Model 5 Jigsaw
RMSD (Pymol) 8.979 1.443 16.502 already running
RMSD (TM-align) 4.72 1.26 5.86 already running
TM-Score 0.60810 0.91279 0.40638 already running
Structural alignment (Pymol)
Superposition by Pymol with the structure predicted by iTasser (Model 3)
Superposition by Pymol with the structure predicted by iTasser (Model 4)
Superposition by Pymol with the structure predicted by iTasser (Model 5)
already running
Structural alignment (TM-align)
Superposition by TM-align with the structure predicted by iTasser (Model 3)
Superposition by TM-align with the structure predicted by iTasser (Model 4)
Superposition by TM-align with the structure predicted by iTasser (Model 5)
already running

TM-Score