Simulations of protein structure were originally based on a hard-sphere potential coupled
with the requirement to avoid steric interactions [Ramachandran, Ramakrishnan, 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 …

Coarse-grained or mesoscopic models of proteins and the corresponding force fields are of
great importance because they enable us to reduce the folding simulation time by several …

The force-matching approach to coarse graining, in which the forces that act on site centers
are fitted to the respective average forces computed from all-atom molecular dynamics …

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 …

A server implementation of the UNRES package (http://www. unres. pl) for coarse-grained
simulations of protein structures with the physics-based UNRES model, coined a name …

We report major algorithmic improvements of the UNRES package for physics‐based coarse‐
grained simulations of proteins. These include (i) introduction of interaction lists to optimize …

Coarse-grained (CG) force fields have become promising tools for studies of protein
behavior, but the balance of speed and accuracy is still a challenge in the research of …

We report the implementation of our united-residue UNRES force field for simulations of
protein structure and dynamics with massively parallel architectures. In addition to coarse …

Molecular dynamics simulations of proteins are usually performed on a single molecule, and
coarse-grained protein models are calibrated using single-molecule simulations, therefore …