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 molecular dynamics trajectories of protein folding or unfolding, generated with the
coarse-grained united-residue force field for the B domain of staphylococcal protein A, were …

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 …

Coarse-grained molecular dynamics simulations offer a dramatic extension of the time-scale
of simulations compared to all-atom approaches. In this article, we describe the use of the …

Protein dynamics take place on many time and length scales. Coarse‐grained structure‐
based \bf(G\overlineo) models utilize the funneled energy landscape theory of protein …

In this work, a double-well network model (DWNM) is presented for generating a coarse-
grained free energy function that can be used to study the transition between reference …

We review the coarse-grained UNited RESidue (UNRES) force field for the simulations of
protein structure and dynamics, which is being developed in our laboratory over the last …

Correlated motions in biomolecules are often essential for their function, for example,
allosteric signal transduction or mechanical/thermodynamic energy transport. Principal …

Structure-based models (SBMs) are simplified models of the biomolecular dynamics that
arise from funneled energy landscapes. We recently introduced an all-atom SBM that …

Protein folding is a fascinating, not fully understood phenomenon in biology. Molecular
dynamics (MD) simulations are an invaluable tool to study conformational changes in …