I was impressed this morning to see that YouTube carries several movies of molecular systems.
Here is one, for example, which shows a protein folding simulation.
Folding a protein takes computer power and science. If you want to know how such a calculation is accomplished, this article on The Molecular Universe provides details: Computers, Molecules and Materials.
Here is another YouTube movie, this one is a combination interview and animation.
In this movie the interviewee compares protein folding to parallel parking, which is an interesting analogy. Then he goes on to compare the protein to a drunken person trying to parallel park, which is even better! However, the video is a little misleading; the protein does not learn how to pack based on its past attempts, as even a drunken parallel parker would. Instead, it is the lowering of the energy of the system which guides the protein into its native configuration.