Difference between revisions of "Homology-modelling HEXA"
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We decided to model the 3D structure with the template structure which has a very low sequence identity. Therefore, we decided to model the structure with 3LUT. Sadly, Swissmodel could not model the structure with this template, because Swissmodel was not able to create an alignment which can be used as basic for the model. Because of this, we decided to calculate a model with 3HN3 as template, which was the next template with a little bit more sequence identity. Therefore, we present here the results of the modelling with 3HN3, whereas by the other methods, we used 3LUT. |
We decided to model the 3D structure with the template structure which has a very low sequence identity. Therefore, we decided to model the structure with 3LUT. Sadly, Swissmodel could not model the structure with this template, because Swissmodel was not able to create an alignment which can be used as basic for the model. Because of this, we decided to calculate a model with 3HN3 as template, which was the next template with a little bit more sequence identity. Therefore, we present here the results of the modelling with 3HN3, whereas by the other methods, we used 3LUT. |
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Revision as of 13:54, 13 June 2011
Contents
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:
Model qualitity:
3LUT:
We decided to model the 3D structure with the template structure which has a very low sequence identity. Therefore, we decided to model the structure with 3LUT. Sadly, Swissmodel could not model the structure with this template, because Swissmodel was not able to create an alignment which can be used as basic for the model. Because of this, we decided to calculate a model with 3HN3 as template, which was the next template with a little bit more sequence identity. Therefore, we present here the results of the modelling with 3HN3, whereas by the other methods, we used 3LUT.
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:
Model qualitity:
Modeller
3BC9:
Modeller calculated one model for 3BC9, which can be seen in the next picture:
3CUI:
Modeller calculated one model for 3CUI, which can be seen in the next picture:
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 | ||||||||
| Structural alignment (TM-align) | |||||||||
| 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) | already running | ||||||||
| Structural alignment (TM-align) | 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) | |||||||||
| Structural alignment (TM-align) | |||||||||
| 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) | already running | ||||||||
| Structural alignment (TM-align) | already running | ||||||||
Results for 3HN3:
| Swissmodel | Modeller | iTasser Model 1 | iTasser Model 2 | ||||||
| RMSD (Pymol) | 27.968 | todo | in queue | in queue | |||||
| RMSD (TM-align) | 4.30 | todo | in queue | in queue | |||||
| TM Score | 0.40661 | todo | in queue | in queue | |||||
| Structural alignment (Pymol) | File:Superpose modeller 3hn3.png Superposition by Pymol with the structure predicted by Modeller |
File:Superpose itasser model1 3hn3.png Superposition by Pymol with the structure predicted by iTasser (Model 1) |
File:Superpose itasser model2 3hn3.png Superposition by Pymol with the structure predicted by iTasser (Model 2) | ||||||
| Structural alignment (TM-align) | File:Tm superpose modeller 3hn3.png Superposition by TM-align with the structure predicted by Modeller |
File:Tm superpose itasser model1 3hn3.png Superposition by TM-align with the structure predicted by iTasser (Model 1) |
File:Tm superpose itasser model2 3hn3.png Superposition by TM-align with the structure predicted by iTasser (Model 2) |
||||||
| iTasser Model 3 | iTasser Model 4 | iTasser Model 5 | Jigsaw | ||||||
| RMSD (Pymol) | in queue | in queue | in queue | todo | |||||
| RMSD (TM-align) | in queue | in queue | in queue | todo | |||||
| TM-Score | in queue | in queue | in queue | todo | |||||
| Structural alignment (Pymol) | in queue | in queue | in queue | todo | |||||
| in queue | in queue | in queue | todo | ||||||
