The structure of a protein is determined by the known laws of physics, other compounds in the solution, and protein's formula (which is a trivial translation of the genetic code for that protein). But it is very computationally expensive to simulate for a large, complicated protein. Watson is a very narrow machine that tries to pretend at answering by using a large database of answers. AFAIK it can't even do trivial new answers (what is the velocity of a rock that fell from the height of 131.5 meters? Wolfram Alpha can answer this, but it is just triggered by the keyword 'fell' and 'height')