This review provides an exposition to the important problems of (i) structure prediction in
protein folding and (ii) de novo protein design. The recent advances in protein folding are …

Coarse-grained (CG) models provide a computationally efficient method for rapidly
investigating the long time-and length-scale processes that play a critical role in many …

Molecular dynamics with coarse-grained models is nowadays extensively used to simulate
biomolecular systems at large time and size scales, compared to those accessible to all …

Exploring recent developments in the field, Coarse-Graining of Condensed Phase and
Biomolecular Systems examines systematic ways of constructing coarse-grained …

Protein folding is considered here by studying the dynamics of the folding of the triple β-
strand WW domain from the Formin-binding protein 28. Starting from the unfolded state and …

We report the application of Langevin dynamics to the physics-based united-residue
(UNRES) force field developed in our laboratory. Ten trajectories were run on seven …

A unified coarse-grained model of three major classes of biological molecules—proteins,
nucleic acids, and polysaccharides—has been developed. It is based on the observations …

We report the modification and parametrization of the united-residue (UNRES) force field for
energy-based protein structure prediction and protein folding simulations. We tested the …

By using principal component analysis (PCA) to examine the molecular dynamics (MD) of
protein folding trajectories, generated with the coarse-grained UNRES force field, for the B …

The multiscale coarse-graining (MS-CG) method is a method for determining the effective
potential energy function for a coarse-grained (CG) model of a system using the data …