Difference between revisions of "Task 4: Homology-based structure prediction"

From Bioinformatikpedia
(HHpred)
(COMA)
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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
  +
!Identity
  +
|-
  +
! >80% Sequence Identity
  +
|-
  +
|1dtw_A
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|8e-59
  +
|100%
  +
|-
  +
|-
  +
! 80-40% Sequence Identity
  +
|-
  +
  +
|-
  +
! <30% Sequence Identity
  +
|-
  +
|2xt6_A
  +
|8.1e-56
  +
|12%
  +
|-
  +
|3duf_A
  +
|2.1e-53
  +
|28%
  +
|-
  +
|3exe_A
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|3.6e-50
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|25%
  +
|-
  +
|3mos_A
  +
|1e-45
  +
|15%
  +
|-
  +
|1l8a_A
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|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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|-
  +
  +
|-
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|}
 
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Revision as of 13:54, 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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