Difference between revisions of "Task 4 Protocol"
From Bioinformatikpedia
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In order to generate the datasets to build the models from we used both the HHpred and COMA web-server. Both tools were applied with default settings. First the the [[Reference sequence (uniprot)]] of BCKDHA was used was used as input, but because these is longer than the actual protein sequence of the PDB entry (1dTW) we decided to directly use the sequence from the PDB ([[Reference Sequence (pdb)]]) for better comparison of the models with the actual structure. As cutoff we only used sequences with an e-vaule smaller than 1e-15. |
In order to generate the datasets to build the models from we used both the HHpred and COMA web-server. Both tools were applied with default settings. First the the [[Reference sequence (uniprot)]] of BCKDHA was used was used as input, but because these is longer than the actual protein sequence of the PDB entry (1dTW) we decided to directly use the sequence from the PDB ([[Reference Sequence (pdb)]]) for better comparison of the models with the actual structure. As cutoff we only used sequences with an e-vaule smaller than 1e-15. |
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Raw output files can be found under: |
Raw output files can be found under: |
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| − | *[http://toolkit.tuebingen.mpg.de/hhpred/results/4987851 HHpred] |
+ | *[http://toolkit.tuebingen.mpg.de/hhpred/results/4987851 HHpred] (old - Uniprot sequence) |
| − | *[http://bioinformatics.ibt.lt:8085/coma/show/results/1922466A71C505375AABF260FC5D381952AC0103 COMA] |
+ | *[http://bioinformatics.ibt.lt:8085/coma/show/results/1922466A71C505375AABF260FC5D381952AC0103 COMA] (old - Uniprot sequence) |
Revision as of 16:38, 3 June 2012
Datasets
In order to generate the datasets to build the models from we used both the HHpred and COMA web-server. Both tools were applied with default settings. First the the Reference sequence (uniprot) of BCKDHA was used was used as input, but because these is longer than the actual protein sequence of the PDB entry (1dTW) we decided to directly use the sequence from the PDB (Reference Sequence (pdb)) for better comparison of the models with the actual structure. As cutoff we only used sequences with an e-vaule smaller than 1e-15. Raw output files can be found under:
