Task 4: Homology-based structure prediction

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Revision as of 14:05, 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 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%
3ey9_A 1.8e-12 11%
2c31_A 1.7e-11 16%
1zpd_A 2.1e-11 12%
3d7k_A 2.7e-11 9%
1upa_A 3.7e-11 10%

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