Difference between revisions of "Task 4: Homology-based structure prediction"
From Bioinformatikpedia
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===COMA=== |
===COMA=== |
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+ | {|class="wikitable" border="1" style="border-spacing:0;text-align: right;" |
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+ | !PDB ID |
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+ | !e-Value |
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+ | !Identity |
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+ | |- |
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+ | ! >80% Sequence Identity |
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+ | |- |
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+ | |1dtw_A |
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+ | |8e-59 |
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+ | |100% |
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+ | |- |
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+ | |- |
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+ | ! 80-40% Sequence Identity |
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+ | |- |
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+ | |||
+ | |- |
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+ | ! <30% Sequence Identity |
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+ | |- |
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+ | |2xt6_A |
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+ | |8.1e-56 |
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+ | |12% |
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+ | |- |
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+ | |3duf_A |
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+ | |2.1e-53 |
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+ | |28% |
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+ | |- |
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+ | |3exe_A |
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+ | |3.6e-50 |
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+ | |25% |
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+ | |- |
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+ | |3mos_A |
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+ | |1e-45 |
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+ | |15% |
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+ | |- |
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+ | |1l8a_A |
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+ | |7.5e-40 |
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+ | |9% |
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+ | |- |
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+ | |3m34_A |
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+ | |1.2e-38 |
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+ | |14% |
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+ | |- |
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+ | |2o1x_A |
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+ | |2.6e-37 |
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+ | |12% |
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+ | |- |
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+ | |3uk1_A |
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+ | |2.4e-33 |
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+ | |15% |
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+ | |- |
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+ | |3ahc_A |
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+ | |1.1e-25 |
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+ | |8% |
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+ | |- |
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+ | |1y9d_A |
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+ | |1e-12 |
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+ | |10% |
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+ | |- |
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+ | |||
+ | |- |
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+ | |} |
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Revision as of 14:54, 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 | Similarity |
---|---|---|---|
>80% Sequence Identity | |||
2BFD | 1.2e-84 | 99% | 1.508 |
80-40% Sequence Identity | |||
1qs0_A | 1.1e-79 | 39% | 0.580 |
<30% Sequence Identity | |||
2ozl_A | 3.6e-71 | 27% | 0.403 |
2yic_A | 1.2e-55 | 14% | 0.116 |
2xt6_A | 2.9e-55 | 14% | 0.121 |
2jgd_A | 4e-55 | 14% | 0.099 |
2o1s_A | 2.1e-27 | 20% | 0.200 |
3kom_A | 2.4e-26 | 18% | 0.148 |
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% |
1y9d_A | 1e-12 | 10% |
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