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

Irbäck, Anders LU and Potthast, Frank LU (1995) In Journal of Chemical Physics 103(23). p.10298-10305
Abstract

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... (More)

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. © 1995 American Institute of Physics.

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publication status
published
in
Journal of Chemical Physics
volume
103
issue
23
pages
8 pages
publisher
American Institute of Physics
external identifiers
  • Scopus:0000773431
ISSN
0021-9606
language
English
LU publication?
yes
id
60beb03b-77b8-4bf8-bf78-076e57acb73e
date added to LUP
2016-08-17 17:59:38
date last changed
2016-10-13 05:12:31
@misc{60beb03b-77b8-4bf8-bf78-076e57acb73e,
  abstract     = {<p>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. © 1995 American Institute of Physics.</p>},
  author       = {Irbäck, Anders and Potthast, Frank},
  issn         = {0021-9606},
  language     = {eng},
  number       = {23},
  pages        = {10298--10305},
  publisher    = {ARRAY(0x9a88f60)},
  series       = {Journal of Chemical Physics},
  title        = {Studies of an off-lattice model for protein folding : Sequence dependence and improved sampling at finite temperature},
  volume       = {103},
  year         = {1995},
}