Though a bit drier than the above mentioned type of docking (dry-dock? ouch ...), docking in computational chemistry is the endeavor of determining how two molecules interact. Molecular interactions are the key to nearly all biological process. proteins, regulating gene transcription. Metals bind to DNA and proteins, affecting structure and function. Hormones bind to receptor proteins on cells, triggering cell responses.

The challenge in docking is determing the most stable way two molecules interact. If you take a lock and key analogy, the docked complex would be the key inserted in the lock. If you're talking about a protein and a horomone, however, the best fit is less obvious. Various computational methods have attacked this problem by trying to define the relative surfaces of the two interacting parties. Then, depending on parameters in a force field, you sample over different interactions until the best one is found.

This sort of technology is coveted by pharmaceutical companies, who are always looking for new drugs to interact with specfic proteins. If they have a way of screening potential drugs on a computer before actually synthesizing them and doing drug trials, it can save a lot of money.