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Estimation of protein folding probability from equilibrium simulations

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F. Rao; G. Settanni; E. Guarnera; A. Caflisch

Journal: J Chem Phys
Year: 2005
Volume: 122
Issue: 18
Pages: 184901
DOI: 10.1063/1.1893753
Type of Publication: Journal Article

Biophysics; Chemistry, Physical; Cluster Analysis; Models, Molecular; Models, Statistical; Models, Theoretical; Monte Carlo Method; Peptides; Probability; Protein Folding; Protein Structure, Secondary; Proteins; Time Factors


The assumption that similar structures have similar folding probabilities (pfold) leads naturally to a procedure to evaluate pfold 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 β-sheet peptide investigated by implicit solvent molecular dynamics simulations.