Task 4: Homology-based structure prediction
From Bioinformatikpedia
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% |
COMA didn't find any hits with sequence similarity between 40% and 80% either, this time however there weren't any hits in close proximity either.