I've worked a little bit with classifying protein folds and a very tiny bit with homology modeling. However, I've heard a lot more recently about intrinsically disordered proteins--proteins that don't really have a regular 3-dimensional structure. Such disordered proteins have been implicated in a variety of functions, so it appears that a regular structure is not necessary for a protein to be biochemically functional.
If I remember homology modeling correctly, most approaches will try their hardest to fit a novel protein to the structure of the closest related homolog, even if it's not a great fit. Is this the case? Say, for example, I have the peptide sequence of an intrinsically disordered protein and I try to predict its structure with homology modeling--I'm going to get some kind of structure in the end, even if it's completely bogus, right?
So my real question is: are there any methods or tools for predicting whether a protein is intrinsically disordered? Such a method/tool could be helpful when predicting protein structure so that you don't force a protein to have a structure it doesn't really have.