Malte Reimold (intermalte) has developed a script that I have been hoping for for some time... the chemical structure conversion script pdb2blend!
Malte's site says it best:
Pdb2blend converts 3d structural molecular data in pdb file format to typical models such as Overlapping Spheres, Sticks or Sticks and Balls in the blender environment.
You might now be thrilled and are ready to start making some nice animations of chemisty in action. But where can you find pdb models to convert? Right here. Check out Malte's BlenderArtist thread for more info.