For many years I participated in a distributed computing project called
Folding@home (f@h) which simulated the folding of proteins to help find cures for diseases such as Alzheimers.
Here is one of the published articles they wrote titled "HOW WELL CAN SIMULATION PREDICT PROTEIN FOLDING KINETICS AND THERMODYNAMICS?"
Too long for me to read, but their conclusions are interesting:
CONCLUSIONS
In the end, an understanding of complex biophysical phenomena will require computer simulation at some level. Most likely, experimental methods will never yield the level of detail that can today be reached with computer simulations. However, the great challenge for simulations is to prove their validity. Thus, it is naturally the combination of powerful simulations with quantitative experimental validation that will elucidate the nature of how proteins fold. How close are we to achieving this goal? In many ways, there has been great progress. The ability to quantitatively predict rates, free energies, and structure from simulations on the basis of physical force fields reflects significant progress made over the past five years. It also draws attention to a new challenge. Even the prediction of experimental observables, such as rates, within experimental uncertainty does not prove that the simulations will yield correct insights into the mechanism of folding. Indeed, recent work suggests that computational models can both agree with experiment and disagree with each other (89). We must therefore push the link between simulation and experiment further by connecting the two with new observables, multiple techniques, and increasingly strict quantitative comparison and validation of simulation methods.Without more detailed experiments, we may not be able to sufficiently test current simulation methodology and the trustworthiness of refined simulations may remain unclear. Nonetheless, the ability to predict rates, free energies, and structure of small proteins is a significant advance for simulation, likely heralding even more significant advances over the next five years.