Based on the coarse‐grained UNRES and NARES‐2P models of proteins and nucleic acids,
respectively, developed in our laboratory, in this work we have developed a coarse‐grained …

Coarse-grained models are useful tools to investigate the structural and thermodynamic
properties of biomolecules. They are obtained by merging several atoms into one interaction …

Physics-based potentials have been developed for the interactions between proteins and
DNA for simulations with the UNRES+ NARES-2P force field. The mean-field interactions …

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 …

Phosphorylated proteins take part in many signaling pathways and play a key role in
homeostasis regulation. The all-atom force fields enable us to study the systems containing …

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 …

Coarse-grained force fields for protein simulations are usually designed and parametrized to
treat proteins composed of natural l-amino acid residues. However, d-amino acid residues …

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 …

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 …

Parameterizing protein coarse-grained models from atomic-level force fields is a relatively
new and promising approach in protein modeling. Here, dihedral angle potentials for the …