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

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 geo metrical properties of the proteins (lattice models), whereas others are co mputationally heavy (traditional molecular dynamics). Results: We used the recently proposed approach of Zhou and Karplus to stud y the folding of a protein model based on the discrete time molecular dynam ics algorithm. We show that this algorithm resolves with respect to time th e folding reversible arrow unfolding transition. In addition, we demonstrat e the ability to study the core of the model protein. Conclusions: The algorithm along with the model of interresidue interaction s can serve as a tool for studying the thermodynamics and kinetics of prote in models.