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

Abstract

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 insensitivity to the geometrical properties of the proteins (lattice models), whereas others are computationally heavy (traditional molecular dynamics).

Results: We used the recently proposed approach of Zhou and Karplus to study the folding of a 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 core of the model protein.

Conclusions: The algorithm along with the model of interresidue interactions can serve as a tool for studying the thermodynamics and kinetics of protein models.