Hello there,
-- I am a python programmer who is interested in automating the drug simulation process. I taught myself about the basics of:
1. Molecular Dynamics
2. Pharmaco Kinetics
3. Pharmaco Dynamics
4. PyMOL
I am planning to create a program that generates all possible combinations of chemicals for the small molecule drug for a given protein. I could not find any source related to the following:
1. How to generate all possible combination of chemicals of drug for the protein? And how the generated chemicals should be represented for the protein-chemical Interaction (chemical structure like CH4 or other format)?
2. How to determine whether the given chemical is an agonist or antagonist computationally? And how to determine whether the viral protein is deactivated for the particular chemical?
3. An example on interaction between a simple viral protein and a chemical drug which deactivates it.
Thanks,
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