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 Post subject: Regarding adding methyl to hydroxyl groups
PostPosted: Sat May 07, 2016 5:13 am 

Joined: Sun May 01, 2016 1:01 am
Posts: 3
Hello everyone!

Just a question about modifying the ligands before we dock them to a protein:

How can we make additions to ligands (in our case, naringenin and quercetin molecules) and do the calculation? Initially we'd like to add methyl groups (-CH3) to the hydroxyls (-OH). I see that the site says we can do that but I haven't been able to figure out how to do it.

If it makes a difference, we are binding to human muscle lactate de-hydrogenase (PDB code: 1i10) and we are looking for inhibitors to this enzyme.

Please let me know, and thanks in advance!
Tim


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 Post subject: Re: Regarding adding methyl to hydroxyl groups
PostPosted: Sat May 07, 2016 10:43 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 204
Hi Tim,

use the draw ligand option, paste the SMILES code of the ligand into the workspace (search for your ligand in PubChem to find the SMILES code) and you will be able to modify the ligand with the built-in drawing tool as you wish.

Zsolt


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 Post subject: Re: Regarding adding methyl to hydroxyl groups
PostPosted: Sun May 08, 2016 2:41 am 

Joined: Sun May 01, 2016 1:01 am
Posts: 3
Hi,

Thank you so much for your reply!
I think I understand how it works, only:

I can't open the ligand in the draw ligand place? It asks me for the protein name and folder and when I input it nothing happens. On the top left hand side of the white box it also says "No valid license found"?

I'm not sure why, but as of now I did it by drawing the entire ligand out by hand and then adding it!
Help would be greatly appreciated;

Thanks,
Tim


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 Post subject: Re: Regarding adding methyl to hydroxyl groups
PostPosted: Sun May 08, 2016 9:32 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 204
Hi,

well, yes, you are right, you can either open a ligand file using upload ligand function or draw a ligand using draw ligand button but there is no halfway at the moment. Earlier it was possible with the built-in Java drawing tool but there was too much complaint that Java was blocked by the browser so we have replaced it to a Javascript editor. We will consider to replace the ligand drawing tool to something that can handle upload and drawing at the same time.

thanks,
Zsolt


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 Post subject: Re: Regarding adding methyl to hydroxyl groups
PostPosted: Sun May 08, 2016 11:20 pm 

Joined: Sun May 01, 2016 1:01 am
Posts: 3
Alright, that makes sense. Thank you so much!

Tim


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