The roles of entropy and kinetics in structure prediction

Background Here we continue our efforts to use methods developed in the folding mechanism community to both better understand and improve structure prediction. Our previous work demonstrated that Rosetta's coarse-grained potentials may actually impede accurate structure prediction at full-atom resolution. Based on this work we postulated that it may be time to work completely at full-atom resolution but that doing so may require more careful attention to the kinetics of convergence. Methodology/Principal Findings To explore the possibility of working entirely at full-atom resolution, we apply enhanced sampling algorithms and the free energy theory developed in the folding mechanism community to full-atom protein structure prediction with the prominent Rosetta package. We find that Rosetta's full-atom scoring function is indeed able to recognize diverse protein native states and that there is a strong correlation between score and Cα RMSD to the native state. However, we also show that there is a huge entropic barrier to folding under this potential and the kinetics of folding are extremely slow. We then exploit this new understanding to suggest ways to improve structure prediction. Conclusions/Significance Based on this work we hypothesize that structure prediction may be improved by taking a more physical approach, i.e. considering the nature of the model thermodynamics and kinetics which result from structure prediction simulations.