During the past decade, advances in drug design (specifically structure-based drug discovery) have seen a lot of success. However, the automated tools for this are encountering a huge problem with the total chemical space that can be sampled.
This is where you, as Foldit players, can help. The immense chemical and conformational space that needs to be sampled is greatly reduced with human spatial recognizing skills, which are far more robust at recognizing patterns than computer algorithms and can intuitively sample conformational and chemical space.
Drug molecules (small molecules) bind to a target molecule (protein in our case) and effect the function of the protein. This change in protein function leads to the desired physiological effect of relieving disease or its symptoms.