Today the majority of biologist are totally accustomed to use the classical 2D schematic drawings to represent the interactions between the different molecules. This approach has been really helpful to simplify the complex reality of the cellular processes but maybe, due to a oversimplification, we are loosing key details that could help us to build a more realistic mental model of the phenomena. Although, another alternatives like animations of 3D molecules models (based in information about the structure) are far away from the typical skills of a biologist.
In this TED Talk, Janet Iwasa show how a open-source program could help to make those animations in a easy way. The program is called “Molecular Flipbox” and can be downloaded totally free.
In my opinion I think that the use of the temporal dimension and more realistic elements could be helpful to avoid the “order” and isolation (from the rest of reactions) that seems to rule in all the pretty molecular books figures and articles. Nevertheless, sometimes a metaphor of some phenomena or a simplification of some elements are indispensable to make more understandable the concept. At the end is necessary the right balance between details and metaphor, and the idea that both depends of the receptor.