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If one would like to control the biological system (e.g. to treat disease or aging/senescence) then one should introduce the drugs in the system, that initiate complex protein interaction pathways that (in final) generate the necessary proteins that induce the necessary biological mechanisms without adverse side effects from additional outcomes.

I am reading https://www.ncbi.nlm.nih.gov/pubmed/29139324 article about application of molecular dynamics simulation to the drug discovery but this article is essentially about simulation of one - target protein/molecule. My question is this: are there methods (molecular dynamics or others) that simulates the processes in the extended protein pathways that are induced by the one or more initiating molecules/drugs? It should be quite complex simulation, but nevertheless nothing less is expected from computational drug discovery and engineering.

I am quite confused. Maybe there is no need for such simulation at all? The databases of protein interactions just provide the more or less complete picture what protein interactions leads to what new proteins or structural updates of participating proteins and there is nothing to simulate - there is just empirical or predicted knowledge about what molecules leads to what other molecules/structures and one just extract the relevant pathway (starting from the drug coming close to the initial proteins) from the database and that is it?

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MD is used for studying structural changes. Simulation of biochemical pathways involves the kinetics (you are not really looking at how enzyme structure changes when it binds to substrate). You can certainly pool all the modelling strategies together to make a hybrid multiscale model.

There are many people who work on such kind of modelling approaches. You can search multiscale modelling and check out recent reviews. This is a somewhat recent (2016) review on multiscale modelling of pharmacokinetics-pharmacodynamics.

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