Folding and mis-folding of peptides and proteins: Insights from molecular simulations

In this paper, the main achievements and problems of the application of
all-atom molecular simulations, with particular attention for Molecular
Dynamics (MD), will be critically reviewed. Starting from unfolding
simulations, through biased simulations, which require a knowledge of
the native state conformation, to folding studies based on the simple
knowledge of the protein (or peptide) sequence, the strengths and
weaknesses of theoretical approaches to the study of folding and their
matching with experimental observations will be discussed. Finally, we
will give a critical outlook on the possible developments of this field
in the near future.