By averaging over atomic details, coarse-grained (CG) models provide profound
computational and conceptual advantages for studying soft materials. In particular, bottom …

Machine learning (ML) has been an important arsenal in computational biology used to
elucidate protein function for decades. With the recent burgeoning of novel ML methods and …

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 …

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 …

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 …

Molecular dynamics with coarse-grained models is nowadays extensively used to simulate
biomolecular systems at large time and size scales, compared to those accessible to all …

We present the BOCS toolkit as a suite of open source software tools for parametrizing
bottom-up coarse-grained (CG) models to accurately reproduce structural and …

Abstract The UNited RESidue (UNRES) force field was tested in the 14th Community Wide
Experiment on the Critical Assessment of Techniques for Protein Structure Prediction …

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 …

Participating as the Cornell-Gdansk group, we have used our physics-based coarse-grained
UNited RESidue (UNRES) force field to predict protein structure in the 11th Community Wide …