  The network paradigm is increasingly used to describe the dynamics of complex
systems. Here we review the current results and propose future development
areas in the assessment of perturbation waves, i.e. propagating structural
changes in amino acid networks building individual protein molecules and in
protein-protein interaction networks (interactomes). We assess the
possibilities and critically review the initial attempts for the application of
game theory to the often rather complicated process, when two protein molecules
approach each other, mutually adjust their conformations via multiple
communication steps and finally, bind to each other. We also summarize
available data on the application of percolation theory for the prediction of
amino acid network- and interactome-dynamics. Furthermore, we give an overview
of the dissection of signals and noise in the cellular context of various
perturbations. Finally, we propose possible applications of the reviewed
methodologies in drug design.
