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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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    $\begingroup$ often there is no specific path of diffusion into the active site - it will tend to be a statistical ensemble of possible paths... $\endgroup$ – shigeta Sep 13 '14 at 2:44
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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.

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