Add medium size Kripo dataset

3D-e-Chem / 3D-e-Chem-VM

Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows

https://3d-e-chem.github.io/3D-e-Chem-VM

Apache License 2.0

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Add medium size Kripo dataset #12

Closed sverhoeven closed 8 years ago

sverhoeven commented 8 years ago

The tiny dataset is not big enough for a comprehensive example. A larger dataset is needed focused on a GPCR family.

sverhoeven commented 8 years ago

Subset available at https://surfdrive.surf.nl/files/index.php/s/mucZMwT97QPuyFL

Created by Searched for 'gpcr' on http://rcsb.org and saved identifiers as 'gpcr_pdbs.tx'.

kripodb fragmentsdb_filter --pdbs gpcr_pdbs.txt Kripo20151223.sqlite kripo-gpcr.sqlite
kripodb distmatrix_filter --fragmentsdb Kripo20151223.sqlite 01-01_to_13-13.out.csi.h5 kripo-gpcr.h5
kripodb fragmentsdb_filter --matrix  kripo-gpcr.h5 Kripo20151223.sqlite kripo-gpcrandhits.sqlite