Browsing by Subject "Generalized ensembles"

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    Secondary structure prediction of beta-hairpin peptide tryptophan zipper-I
    (2008) Gökoǧlu G.; Çelik, T.
    We have investigated the folding properties of tryptophan zipper-I molecule which folds into a stable β-hairpin motif in aqueous solution as suggested by nuclear magnetic resonance (NMR) experiments. An all-atom presentation, including hydrogen, was used with an implicit solvent. As a simulation technique, simulated tempering algorithm was used to obtain equilibrium conformations of the molecule at ten distinct temperatures. Our minimum energy configuration obtained from simulated tempering algorithm is a β-hairpin motif with 1.30 Å backbone root-mean-square deviation from the reference PDB structure (1le0.pdb). Several quantities and exhaustive folding free energy landscapes were determined and discussed in order to clarify the folding behavior. © 2008 Elsevier Ltd. All rights reserved.