Discrete molecular dynamics studies of the folding of a protein-like model

Details Discrete molecular dynamics studies of the folding of a protein-like model Discrete molecular dynamics studies of the folding of a protein-like model

1998-12-17

arxiv.org/abs/cond-mat/9812291v1

Folding & Design 3: 577--587 (1998)

Physics

Condensed Matter

Statistical Mechanics

15 pages including 20 figures (Folding & Design in press)

Scientific paper

Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical properties of the proteins (lattice models), while others are computationally heavy (traditional MD). Results: We use a recently-proposed approach of Zhou and Karplus to study the folding of the protein model based on the discrete time molecular dynamics algorithm. We show that this algorithm resolves with respect to time the folding --- unfolding transition. In addition, we demonstrate the ability to study the coreof the model protein. Conclusion: The algorithm along with the model of inter-residue interactions can serve as a tool to study the thermodynamics and kinetics of protein models.

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