Difference between revisions of "Task 4: Homology-based structure prediction"
From Bioinformatikpedia
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===HHpred=== |
===HHpred=== |
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{|class="wikitable" border="1" style="border-spacing:0;text-align: right;" |
{|class="wikitable" border="1" style="border-spacing:0;text-align: right;" |
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| + | !PDB ID |
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| − | !Region |
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| + | !e-Value |
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| − | !PolyPhobius Start |
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| + | !Identity |
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| − | !Stop |
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| + | !Similarity |
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| − | !UniProt Start |
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| − | !Stop |
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| − | !OPM Start |
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| − | !Stop |
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| − | !PDBTM Start |
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| − | !Stop |
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|- |
|- |
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| + | ! >80% Sequence Similarity |
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| − | |1.transmembrane |
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| − | |30 |
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| − | |55 |
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| − | |33 |
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| − | |55 |
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| − | |34 |
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| − | |52 |
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| − | |35 |
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| − | |52 |
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|- |
|- |
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| + | |2BFD |
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| − | |2.transmembrane |
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| + | |1.2e-84 |
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| − | |66 |
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| − | | |
+ | |99% |
| + | |1.508 |
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| − | |66 |
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| − | |88 |
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| − | |67 |
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| − | |91 |
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| − | |68 |
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| − | |84 |
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|- |
|- |
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| − | |3.transmembrane |
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| − | |105 |
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| − | |126 |
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| − | |105 |
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| − | |126 |
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| − | |101 |
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| − | |126 |
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| − | |109 |
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| − | |123 |
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|- |
|- |
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| + | ! 80-40% Sequence Similarity |
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| − | |4.transmembrane |
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| − | |150 |
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| − | |170 |
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| − | |150 |
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| − | |170 |
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| − | |150 |
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| − | |170 |
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| − | |152 |
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| − | |166 |
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|- |
|- |
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| + | |1qs0_A |
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| − | |5.transmembrane |
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| + | |1.1e-79 |
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| − | |188 |
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| − | | |
+ | |39% |
| + | |0.580 |
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| − | |188 |
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| − | |212 |
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| − | |187 |
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| − | |209 |
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| − | |191 |
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| − | |206 |
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|- |
|- |
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| + | ! <30% Sequence Similarity |
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| − | |6.transmembrane |
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| − | |329 |
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| − | |352 |
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| − | |330 |
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| − | |351 |
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| − | |330 |
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| − | |351 |
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| − | |334 |
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| − | |347 |
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|- |
|- |
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| + | |1w85_A |
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| − | |7.transmembrane |
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| + | |3.6e-76 |
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| − | |367 |
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| + | |32% |
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| − | |386 |
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| + | |0.576 |
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| − | |367 |
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| − | |388 |
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| − | |363 |
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| − | |386 |
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| − | |368 |
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| − | |382 |
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|- |
|- |
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| + | |||
|} |
|} |
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Revision as of 14:10, 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 Similarity | |||
| 2BFD | 1.2e-84 | 99% | 1.508 |
| 80-40% Sequence Similarity | |||
| 1qs0_A | 1.1e-79 | 39% | 0.580 |
| <30% Sequence Similarity | |||
| 1w85_A | 3.6e-76 | 32% | 0.576 |
COMA
blah
