Difference between revisions of "Homology-modelling HEXA"
From Bioinformatikpedia
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=== Modeller === |
=== Modeller === |
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| − | We used Modeller from the command line. Therefore we followed the instructions, described [[ |
+ | We used Modeller from the command line. Therefore we followed the instructions, described [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Task_4:_Homology_based_structure_predictions#Homology_modelling_with_Modeller 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. |
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. |
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| − | For Modeller we used the Pir Alignment format, which can be found here: [[ |
+ | For Modeller we used the Pir Alignment format, which can be found here: [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Homology-modelling_HEXA/3bc9.pir 3BC9]], [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Homology-modelling_HEXA/3cui.pir 3CUI]], [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Homology-modelling_HEXA/3lut.pir, 3LUT]] |
=== iTasser === |
=== iTasser === |
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Revision as of 14:30, 11 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 |
Results
Swissmodel
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]
