Task 4: Homology-based structure prediction

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Revision as of 14:42, 30 May 2012 by Wagnerr (talk | contribs) (COMA)

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.