Difference between revisions of "Fabry:Homology based structure predictions/Journal"
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== Dataset preparation == |
== Dataset preparation == |
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| − | The homology search was performed online and resulted in the two output files [https://www.dropbox.com/s/4ue1umheukk7j1a/hhpred.out.txt hhpred.out] and [https://www.dropbox.com/s/ycfy8ke6xt3ofrp/coma.out.txt coma.out] for the structure search with [http://toolkit.tuebingen.mpg.de/hhpred HHpred] and [http://bioinformatics.ibt.lt:8085/coma/ COMA], respectively. In both cases, we used the default values, thresholds and databases. |
+ | The homology search was performed online and resulted in the two output files [https://www.dropbox.com/s/4ue1umheukk7j1a/hhpred.out.txt hhpred.out] and [https://www.dropbox.com/s/ycfy8ke6xt3ofrp/coma.out.txt coma.out] for the structure search with [http://toolkit.tuebingen.mpg.de/hhpred HHpred] and [http://bioinformatics.ibt.lt:8085/coma/ COMA], respectively. In both cases, we used the default values, thresholds and databases. |
| − | From |
+ | From both the resulting files we tried in each case to create three distinct datasets with the demanded sequence identity to the target protein with the following calls and scripts. |
perl [https://www.dropbox.com/s/8vu2mnnl733f3zh/make_dataset_hhpred.pl.txt make_dataset_hhpred.pl] [https://www.dropbox.com/s/4ue1umheukk7j1a/hhpred.out.txt hhpred.out] 0.0000000000000001 |
perl [https://www.dropbox.com/s/8vu2mnnl733f3zh/make_dataset_hhpred.pl.txt make_dataset_hhpred.pl] [https://www.dropbox.com/s/4ue1umheukk7j1a/hhpred.out.txt hhpred.out] 0.0000000000000001 |
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Revision as of 01:04, 23 May 2012
Fabry Disease » Homology based structure predictions » Journal
Contents
Dataset preparation
The homology search was performed online and resulted in the two output files hhpred.out and coma.out for the structure search with HHpred and COMA, respectively. In both cases, we used the default values, thresholds and databases. From both the resulting files we tried in each case to create three distinct datasets with the demanded sequence identity to the target protein with the following calls and scripts.
perl make_dataset_hhpred.pl hhpred.out 0.0000000000000001
This resulted in the HHpred datasets mentioned in Dataset preparation Table 1 and the corresponding pdb structure files.
perl make_dataset_coma.pl coma.out 0.002
This resulted in the Coma datasets mentioned in Dataset preparation Table 2 and the corresponding pdb structure files.
