The folding mechanism of β-hairpins might provide fundamental knowledge that helps us to
understand how large proteins fold. However, all-atom molecular dynamics is difficult to do …

Reduction of the representation of macromolecular systems such as, eg biopolymers from
an all-atom to a more crude one, which is termed coarse-graining, is usually regarded as a …

Serum amyloid A (SAA) is a multifunctional acute‐phase protein whose concentration in
serum increases markedly following a number of chronic inflammatory and neoplastic …

Protein structure prediction methods typically use statistical potentials, which rely on
statistics derived from a database of know protein structures. In the vast majority of cases …

The kinetic-trapping problem in simulating protein folding can be overcome by using a
Replica Exchange Method (REM). However, in implementing REM in molecular dynamics …

UNRES is a coarse-grained model of polypeptide chains. Until now, each version of UNRES
(UNRESPACK v. 3.2 and earlier ones) has been written in Fortran 77. Due to the fact that …

We have investigated the folding of two helix-bundle proteins, 36-residue Villin headpiece
and 56-residue E-domain of Staphylococcal protein A, by combining molecular dynamics …

Understanding the functioning of living cells requires knowledge of structure and long-time
dynamics of proteins and other biological macromolecules, which information is not readily …

Automatic protein structure predictors use the notion of energy to guide the search towards
good candidate structures. The energy functions used by the state-of-the-art predictors are …

The relevance of describing complex systems by simple coarse-grained models lies in the
separation of time scales between the coarse-grained and fine or secondary degrees of …