[DIYbio] Re: Chemical Structure Generation for Drug Simulation

AFAIK there's no API for that. If there were, I suspect it would be forced to make a lot of assumptions that would sacrifice a significant deal of accuracy for speed and ease-of-use. Typically this type of experiment requires a good deal of hand-holding, as there are decisions that need to be made wisely at many steps of the project.

For instance, even once you have the PDB file for HIV Protease, you need to make decisions about how to represent Hydrogens on some of the more volatile amino acids, based on such considerations as PH.

Also, you mention having the PDB file for HIV. Do you mean to say a specific HIV protein? I guessed protease because that's very common. Simulating an entire HIV capsid is a massive task (see: http://www.isgtw.org/feature/64-million-atom-simulation-%E2%80%93-new-weapon-against-hiv). Additionally, performing a binding affinity experiment in the context of an entire capsid is unnecessary - generally these simulations only include the protein and small molecule in question. Although it's possible that interactions from other proteins may affect the binding affinity, performing this sort of simulation across an entire capsid would be impossible, because you'd need an extremely long simulation at a massive scale to account for the flexibility and size of the system.

Best,
Tom Weingarten

On Monday, March 30, 2015 at 10:39:25 PM UTC-4, Gokula Krishna wrote:
I have a Molecule in SMILES format, eg., Zidovudine: Cc1cn(c(=O)[nH]c1=O)[C@H]2C[C@@H]([C@H](O2)CO)N=[N+]=[N-]
And the PDB file for HIV. How to calculate binding affinity computationally? Is there any API?

On Friday, March 13, 2015 at 11:13:56 PM UTC+5:30, Gokula Krishna wrote:
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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