Is there any simulation protocol or paper which can simulate the dynamics of drug entry and interaction with the target protein?
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This is a tough topic, have a look at the following references and see, if they can help you:
Absolutely, the two I've had the most success are working with a radiolabeled and a fluorescently labeled version of the drug. Many drugs autofluoresce as well and this can be easily tracked.
When it's labeled as mentioned above microscopy or a luminometer, spectrophomoter or a scintillation counter can evaluate fractions or whole cells, or purified binding substrates.