G. Colombo and C. Micheletti
Protein folding simulations: combining coarse-grained models
and all-atom molecular dynamics
Theor. Chem. Acc.116 75-86 (2006)
Link to online article.
The investigation of protein folding and its ramifications
in biological contexts is at the heart of molecular
biology. Theoretical and computational studies provide a
steadily growing contribution to the understanding of factors
driving a given polypeptide sequence into the native state.
Simplified coarse-grained protein models have proven very
useful to gain insights into the general thermodynamic and
kinetic features of the folding process. On the other hand, allatom
simulations allowto follow, with microscopic detail, the
delicate interplay of the various chemical interactions leading
to the formation of the native or intermediate states. In
this paper we will discuss different computational strategies
employed to tackle the protein folding problem, based on the
use of either coarse-grained or all-atom protein descriptions.
Finallywewill discuss a recent approach that allows to extend
the reach of ordinary folding simulations by using a simplified
description of protein structures and energy functional
in conjunction with all-atom molecular dynamics.