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- Title
Global optimization and folding pathways of selected alpha-helical proteins.
- Authors
Carr, Joanne M; Wales, David J
- Abstract
The results of basin-hopping global optimization simulations are presented for four small, alpha-helical proteins described by a coarse-grained potential. A step-taking scheme that incorporates the local conformational preferences extracted from a large number of high-resolution protein structures is compared with an unbiased scheme. In addition, the discrete path sampling method is used to investigate the folding of one of the proteins, namely, the villin headpiece subdomain. Folding times from kinetic Monte Carlo simulations and iterative calculations based on a Markovian first-step analysis for the resulting stationary-point database are in good mutual agreement, but differ significantly from the experimental values, probably because the native state is not the global free energy minimum for the potential employed.
- Publication
The Journal of chemical physics, 2005, Vol 123, Issue 23, p234901
- ISSN
0021-9606
- Publication type
Journal Article
- DOI
10.1063/1.2135783