CASP (Critical Assessment of Techniques for Protein Structure Prediction) is a protein structure prediction competition that is held every 2 years, with labs from around the world testing out their newest state-of-the-art folding methods on unpublished structures. Puzzles in this category are based on the CASP11 competition targets. To find out more about CASP, try http://en.wikipedia.org/wiki/CASP or the CASP11 website at http://predictioncenter.org/casp11
In Predicted Contacts Puzzles, we have predictions for which residues should be close together, or "in contact". These contacts are shown on the Contact Map panel. In addition to this visualization, most Contact puzzles will give you a bonus for matching the predicted contacts.
For small molecule design puzzles, players are tasked to design inhibitors or modulators for proteins that are of therapeutic interest. This is different from protein design in that the chemical space space that can be enumerated is estimated at 10^60. Designing small molecules involves modifying individual atoms, adding and deleting fragments, and using reaction-based design for tractable synthesis of the small molecule.