This review presents a collection of coupled experimental/computational studies taken from our own experience in the field of self-assembled dendrimers for heparin binding. These studies emphasize both the potentiality played by this hybrid methodology to the design, synthesis and development of possible protamine replacers in biomedical applications, and the obstacles this field has still overcome before these molecules can be translated into nanomedicines available in clinical settings. To date, reliable multiscale molecular simulations may be easier to perform than experiments. Accordingly, the synergist action of computer modeling and dedicated experiments can dramatically help in reducing the time and costs of the pre- and post-development stages of nanomedicines.