Theoretical studies of nucleic acids and nucleic acid-protein complexes using charmm

Abstract

Empirical force field calculations of nucleic acids have become a standard method for studying the relationship of structure and dynamics to the activity of these biologically essential molecules. One of the major tools used to perform such calculations is the program CHARMM along with the CHARMM all-atom force fields designed for biomolecules, including nucleic acids. In this chapter the utility of CHARMM and the associated empirical force field as a modeling tool to study nucleic acids is presented. In addition, an overview of studies performed using these utilities is presented. © 2006 Springer.