Application of molecular dynamics simulation (or alternatives) for the full pathways of protein interactions?
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.