[DIYbio] Re: Chemical Structure Generation for Drug Simulation

 certainly it sounds like a  mammoth project but it is definitely possible and need of the hour  to  develop  search automation models

 to increase the pace in new age  drug research.  rather than  measuring the project the scale of no of phd thesis  I suggest this could be 

 quickly done  by  aggregating efforts of passionate  people   from both it and biotechnology as a collaborative  sourcing (opensource )

 what if you thoughts  i am also putting  my intent  to participate  in such  opensource project.. 

 coming to me i did my masters in biochemistry and i have  working knowledge  in python

 good luck

 Supreet Kaur

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,