protein -ligand docking

i cant find ligand in ChEMBL to create a compound, so I use PubChem Download but how can I insert Compound library to my data to continue the protein-ligand docking tutorial


What do you mean with you can not find a compound? Do you get an error or just no compound? Which query have you used in your chembl tool?


Generate compound library

  1. Compound conversion tool with the following parameters:
  • param-file “Molecular input file” : ‘Ligand’ PDB file
  • param-file “Output format” : SMILES format (SMI)
  • Leave all other options as default.
  1. Rename the output of the ‘compound conversion’ step to ‘Ligand SMILES’ .
    Search ChEMBL database tool with the following parameters:
  • param-file “SMILES input type” : File
  • param-file “Input file” : ‘Ligand SMILES’ file
  • param-file “Search type” : Similarity
  • param-file “Tanimoto cutoff score” : 80
  • param-file “Filter for Lipinski’s Rule of Five” : Yes
    the output of that file =0 so i search by the output of liand SMILE file in Pubchem site and found the compound for that output but i need to do that step inside Galaxy to continue the rest of procedures to make docking.

Can you please check that your

file, only has one column? The SMILES string. Thanks.

yes, one column I cut the second column

Hello @Ersaa_Mamdouh_Hisham. I guess you are not using the compound from the tutorial here:

If not, it may be that the chembl database simply doesn’t have any compounds which are similar to yours.

If you already have a list of SMILES for docking (or just 1), you can upload the file to Galaxy and continue with the next step.

I saw you have the Tanimoto coefficient set to 80, you could try to lower it to 70 and see if you get any results.

I set Tanimoto coefficient to 70, still same the file empty but when searching at I found more than 100 compounds for my ligand PDB so I need to upload each SMILES separately? I also use the function of PubChem Download on galaxy but how can i search inside it while using galaxy and extract SMILES file?

i upload the compound files from pubChem , now u need to
visualize the compounds generated, the problem is it depends on a compound found in

ChEMBL pelt in galaxy which i not found on it the compound in the first place so how can i use the function of (visualizing)depend on pubchem.