Difference between revisions of "Task 4: Homology-based structure prediction"
From Bioinformatikpedia
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| − | |1y9d_A |
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| − | |1e-12 |
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| − | |10% |
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| − | |3ey9_A |
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| − | |1.8e-12 |
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| − | |11% |
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| − | |2c31_A |
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| − | |1.7e-11 |
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| − | |16% |
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| − | |1zpd_A |
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| − | |2.1e-11 |
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| − | |12% |
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| − | |- |
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| − | |3d7k_A |
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| − | |2.7e-11 |
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| − | |9% |
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| − | |- |
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| − | |1upa_A |
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| − | |3.7e-11 |
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| − | |10% |
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Revision as of 15:39, 30 May 2012
More detailed information about the generation of the results can be found in the Task 4 Protocol.
Datasets
In order to generate a model for our protein we first need to find homologous structures on which we base our model on. For this task we use HHpred and COMA.
HHpred
| PDB ID | e-Value | Identity |
|---|---|---|
| >80% Sequence Identity | ||
| 2BFD | 1.2e-84 | 99% |
| 80-40% Sequence Identity | ||
| 1qs0_A | 1.1e-79 | 39% |
| <30% Sequence Identity | ||
| 2ozl_A | 3.6e-71 | 27% |
| 2yic_A | 1.2e-55 | 14% |
| 2xt6_A | 2.9e-55 | 14% |
| 2jgd_A | 4e-55 | 14% |
| 2o1s_A | 2.1e-27 | 20% |
| 3kom_A | 2.4e-26 | 18% |
| 3m49_A | 2.4e-26 | 18% |
| 1gpu_A | 2.3e-26 | 18% |
| 2e6k_A | 1.1e-26 | 20% |
| 3l84_A | 6.4e-26 | 17% |
| 2r8o_A | 1.9e-25 | 20% |
| 3uk1_A | 2.6e-25 | 19% |
| 3rim_A | 1.2e-24 | 18% |
| 1r9j_A | 5.7e-24 | 17% |
| 2o1x_A | 1e-25 | 15% |
| 1itz_A | 7.4e-23 | 20% |
| 3mos_A | 2.3e-22 | 19% |
| 2qtc_A | 1.5e-21 | 16% |
| 3ahc_A | 7.2e-16 | 16% |
Unfortunately the HHpred search did not produce any hits with a sequence identity between 40% and 80%. For testing purposes we assume 1qs0_A to fit in that category.
COMA
| PDB ID | e-Value | Identity |
|---|---|---|
| >80% Sequence Identity | ||
| 1dtw_A | 8e-59 | 100% |
| 80-40% Sequence Identity | ||
| <30% Sequence Identity | ||
| 2xt6_A | 8.1e-56 | 12% |
| 3duf_A | 2.1e-53 | 28% |
| 3exe_A | 3.6e-50 | 25% |
| 3mos_A | 1e-45 | 15% |
| 1l8a_A | 7.5e-40 | 9% |
| 3m34_A | 1.2e-38 | 14% |
| 2o1x_A | 2.6e-37 | 12% |
| 3uk1_A | 2.4e-33 | 15% |
| 3ahc_A | 1.1e-25 | 8% |
blah
