ABSTRACT
This chapter summarizes the theoretical principles of the construction of physics-based coarse-grained force fields. It describes the UNited-RESidue (UNRES) force field, together with its recent extensions to treat disulfide bonds, cis–trans isomerization of peptide groups, and D-amino-acid residues. The chapter explains its molecular dynamics (MD) implementation, and its applications in physics-based prediction of protein structures, analysis of protein free-energy landscapes (FELs), and description of protein folding in terms of kinks as well as applications to study biological problems. It discusses the derivation and parameterization of the respective UNRES energy-function components. The derivation of the UNRES energy terms was accomplished by the cluster-cumulant approach. The chapter describes the recently developed potentials for protein–nucleic acid interactions. Dynamic formation and breaking of disulfide bonds are a part of the folding of many proteins such as, e.g., bovine pancreatic trypsin inhibitor and ribonuclease. The chapter concludes the chapter by describing perspectives for further applications and software availability, respectively.
