A long standing problem in structural bioinformatics is to determine the three-dimensional (3-
D) structure of a protein when only a sequence of amino acid residues is given. Many …

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 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 …

A variety of coarse-grained (CG) models exists for simulation of proteins. An outstanding
problem is the construction of a CG model with physically accurate conformational …

Coarse-grained protein models with various levels of granularity and degrees of freedom
offer the possibility to explore many phenomena including folding, assembly, and …

We describe here the PRIMO (protein intermediate model) force field, a physics-based fully
transferable additive coarse-grained potential energy function that is compatible with an all …

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 …

The growth mechanism of β-amyloid (Aβ) peptide fibrils was studied by a physics-based
coarse-grained united-residue model and molecular dynamics (MD) simulations. To identify …

The protein structure prediction problem continues to elude scientists. Despite the
introduction of many methods, only modest gains were made over the last decade for certain …

The unfolded state of proteins presents many challenges to elucidate the structural basis for
biological function. This state is characterized by a large degree of structural heterogeneity …