Re: Well ...
The problem is really basic science. It's possible now to homology model a modest single domain protein in a few hours even on a desktop workstation. Understanding how the current algorithms and model assumptions fail is MUCH harder. In the end a protein is a dynamic entity and that makes it all much harder.
A few years ago I was interested in a kinase enzyme. A xtal structure was available but the reality turned out that the protein was in dynamic equilibrium between ( at least ) two forms. One was equivalent to the xtal structure, the other was a form that could be activated to give the (unstable) working form - what the structure of that was ???.
The whole reason to model proteins is to make use of the information gained - a fast method of getting the wrong, non-physiological answer is useless on it's own. I'm very optimistic really but there are many problems to solve that don't depend on calculation speed.