Estimation of protein folding probability from equilibrium simulations

TitleEstimation of protein folding probability from equilibrium simulations
Publication TypeJournal Article
Year of Publication2005
AuthorsRao F., Settanni G., Guarnera E., Caflisch A.
JournalJournal of Chemical Physics
Volume122
Issue18
Pagination184901
Date Published2005 May 8
Type of ArticleResearch Article
ISSN0021-9606
KeywordsBiophysics, Chemistry, Physical, Cluster Analysis, Models, Molecular, Models, Statistical, Models, Theoretical, Monte Carlo Method, Peptides, Probability, Protein Folding, Protein Structure, Secondary, Proteins, Time Factors
Abstract

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.

DOI10.1063/1.1893753
pubindex

0066

Alternate JournalJ Chem Phys
PubMed ID15918759
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