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PostPosted: Wed Mar 02, 2016 12:28 pm 
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Joined: Wed Mar 02, 2016 12:17 pm
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Dear All,

I apologize if this topic was previously brought up, but I truly cannot find the correct answer in here.

WHAT WE ARE TRYING TO DO?

First, just to describe the context, we are trying to train deep learning network for some medchem purposes. To this end, we downloaded all the protein:small molecule ligand complexes from PDB. At the current stage, we'd like to generate the restrain files for all of these complexes.

CHALLENGE

At the moment, we are struggling with generation of the interaction parameters between proteins and small molecules. I assume that the only way to go here, is to dock all these ligands and generate parameter/restrain files from the docked molecules (those docked complexes with best score). My question is if there is and efficient way to generate interaction parameters for more than 10,000 structures of complexes?

Best wishes.


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