protein -ligand docking

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1

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

2

Hi,

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?

Cheers,
Bjoern

3

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.
4

Can you please check that your

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

5

yes, one column I cut the second column

6

Hello @Ersaa_Mamdouh_Hisham. I guess you are not using the compound from the tutorial here: https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html?

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.

7

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.

8

I set Tanimoto coefficient to 70, still same the file empty but when searching at PubChem.com 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?

9

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.