Zauberkugel

Annotation: Protein target prediction of a bioactive ligand with Align-it and ePharmaLib

StepAnnotation
Step 1: Input dataset
select at runtime
Upload an .smi file containing the isomeric SMILES (first column) and name (second column) of a single query ligand; both columns separated by a tab.
Step 2: Input dataset
select at runtime
Fetch the ePharmaLib dataset from the internet under the URL: `https://zenodo.org/record/5898113/files/ePharmaLib_PHARAO_human.phar` .
Step 3: Add hydrogen atoms
Output dataset 'output' from step 1
True
7.4
Step 4: Split file
Generic
Output dataset 'output' from step 2
Specify record separator as regular expression
\$\$\$\$
After
Number of records per file ('chunk mode')
1
epharmalib
Maintain record order
Step 5: RDConf: Low-energy ligand conformer search
Output dataset 'outfile' from step 3
100
1
9162006
0.7
10.0
False
False
False
Step 6: Pharmacophore alignment
Output dataset 'outfile' from step 5
Output dataset 'list_output_generic' from step 4
aromatic rings hydrogen bond donors hydrogen bond acceptors lipophilic spots charge centers
0.5
False
True
True
False
False
SMILES
0.5
1
TVERSKY_REF
Step 7: Concatenate datasets
Output dataset 'score_result_file' from step 6
Datasets
Step 8: Sort
Output dataset 'out_file1' from step 7
10
Numerical sort
Descending order
Column selections
0