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Anders Irbäck. Photo.

Anders Irbäck

Professor

Anders Irbäck. Photo.

Studies of an off-lattice model for protein folding : Sequence dependence and improved sampling at finite temperature

Author

  • Anders Irbäck
  • Frank Potthast

Summary, in English

We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two dimensional and has two different "amino acids." Using numerical simulations of all chains containing eight or ten monomers, we examine the sequence dependence at a fixed temperature. It is shown that only a few of the chains exist in unique folded state at this temperature, and the energy level spectra of chains with different types of behavior are compared. Furthermore, we use this model as a testbed for two improved Monte Carlo algorithms. Both algorithms are based on letting some parameter of the model become a dynamical variable; one of the algorithms uses a fluctuating temperature and the other a fluctuating monomer sequence. We find that by these algorithms one gains large factors in efficiency in comparison with conventional methods.

Department/s

  • Computational Biology and Biological Physics
  • Department of Astronomy and Theoretical Physics

Publishing year

1995

Language

English

Pages

10298-10305

Publication/Series

Journal of Chemical Physics

Volume

103

Issue

23

Document type

Journal article

Publisher

American Institute of Physics (AIP)

Status

Published

ISBN/ISSN/Other

  • ISSN: 0021-9606