title: Folding probabilities: a novel approach to folding transitions and the two-dimensional Ising-model.
abstract: The theoretical concept of folding probability, p(fold), has proven to be a useful means to characterize the kinetics of protein folding. Here, we illustrate the practical importance of p(fold) and demonstrate how it can be determined theoretically. We derive a general analytical expression for p(fold) and show how it can be estimated from simulations for systems where the transition rates between the relevant microstates are not known. By analyzing the Ising model we are able to determine the scaling behavior of the numerical error in the p(fold) estimate as function of the number of analyzed Monte Carlo runs. We apply our method to a simple, newly developed protein folding model for the formation of alpha helices. It is demonstrated that our technique highly parallelizes the calculation of p(fold) and that it is orders of magnitude more efficient than conventional approaches.
authors.affiliation: Lyman Laboratory of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Lenz
authors.forename: Bojan
authors.initials: B
authors.lastname: Zagrovic
authors.forename: Jessica
authors.initials: J
authors.lastname: Shapiro
authors.forename: Vijay S
authors.initials: VS
authors.lastname: Pande
mesh_terms: D000465:Algorithms; D007700:Kinetics; D008956:Models, Chemical; D009010:Monte Carlo Method; D011336:Probability; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins