Coarse-Grained Modeling of the Interplay between Secondary Structure Propensities and Protein Fold Assembly.

We recently developed a new coarse-grained model of protein structure and dynamics [ Dawid et al. J. Chem.

SURPASS Low-Resolution Coarse-Grained Protein Modeling.

Coarse-grained modeling of biomolecules has a very important role in molecular biology. In this work we present a novel SURPASS (Single United Residue per Pre-Averaged Secondary Structure fragment) model of proteins that can be an interesting alternative for existing coarse-grained models. The design of the model is unique and strongly supported by the statistical analysis of structural regularities characteristic for protein systems.

Coarse-Grained Protein Models and Their Applications.

The traditional computational modeling of protein structure, dynamics, and interactions remains difficult for many protein systems. It is mostly due to the size of protein conformational spaces and required simulation time scales that are still too large to be studied in atomistic detail. Lowering the level of protein representation from all-atom to coarse-grained opens up new possibilities for studying protein systems.