title: How well can simulation predict protein folding kinetics and thermodynamics?
abstract: Simulation of protein folding has come a long way in five years. Notably, new quantitative comparisons with experiments for small, rapidly folding proteins have become possible. As the only way to validate simulation methodology, this achievement marks a significant advance. Here, we detail these recent achievements and ask whether simulations have indeed rendered quantitative predictions in several areas, including protein folding kinetics, thermodynamics, and physics-based methods for structure prediction. We conclude by looking to the future of such comparisons between simulations and experiments.
authors.affiliation: Biophysics Program, Stanford University, Stanford, California 94305, USA. csnow@alum.mit.edu
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Snow
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Sorin
authors.forename: Young Min
authors.initials: YM
authors.lastname: Rhee
authors.forename: Vijay S
authors.initials: VS
authors.lastname: Pande
mesh_terms: D001703:Biophysics / Q000379:methods*; D003198:Computer Simulation; D003201:Computers; D007700:Kinetics; D015233:Models, Statistical; D008962:Models, Theoretical; D017510:Protein Folding; D012997:Solvents / Q000737:chemistry; D013696:Temperature; D013997:Time Factors; D014867:Water / Q000737:chemistry
chemical_list: D012997:Solvents; D014867:Water