Estimation of protein folding probability from equilibrium simulations

Abstract

The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide or protein. The procedure utilizes a structurally homogeneous clustering and does not require any additional simulation. It can be used to detect multiple folding pathways as shown for a three-stranded antiparallel $\beta$-sheet peptide investigated by implicit solvent molecular dynamics simulations.