By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …

Coarse-grained models are emerging as a practical alternative to all-atom simulations for
the characterization of protein folding mechanisms over long time scales. While a decade …

A generalized understanding of protein dynamics is an unsolved scientific problem, the
solution of which is critical to the interpretation of the structure-function relationships that …

Coarse-grained (CG) molecular simulations have become a standard tool to study molecular
processes on time and length scales inaccessible to all-atom simulations. Parametrizing CG …

Many biologically interesting phenomena occur on a time scale that is too long to be studied
by atomistic simulations. These phenomena include the dynamics of large proteins and self …

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

We present a multiscale method for the determination of collective reaction coordinates for
macromolecular dynamics based on two recently developed mathematical techniques …

We propose a method of quantifying the degree of frustration manifested by spatially local
interactions in protein biomolecules. This method of localization smoothly generalizes the …

The definition of reaction coordinates for the characterization of a protein-folding reaction
has long been a controversial issue, even for the “simple” case in which one single free …

1. Introduction 22. The macroscopic and microscopic views of protein folding 22.1 The
macroscopic view: the experimental folding free-energy profile 22.2 The microscopic view …