Evolution imposes constraints on the design of proteins and we have been using computational methods, in particular MD simulations, to understand the folding, and in turn the design of proteins. Specifically, since the same amino acid sequence encodes both the folding and the function of proteins, we find that functional regions, such as binding and active sites, modulate the folding of proteins. Using different example proteins, I will illustrate the diverse effects that function (mainly binding sites) has on the folding of proteins and the methods that we use to identify and understand these effects.