Format

Send to:

Choose Destination
See comment in PubMed Commons below
J Chem Phys. 2005 Dec 15;123(23):234901.

Global optimization and folding pathways of selected alpha-helical proteins.

Author information

  • 1University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

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.

PMID:
16392943
[PubMed - indexed for MEDLINE]
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for American Institute of Physics
    Loading ...
    Write to the Help Desk