The Use of Molecular Dynamics and Free Energy Perturbation Approaches in Simulating the Properties of Macromolecules and Their Binding to Ligands

Abstract

In this article we present a review of the use of molecular dynamics in simulating the properties of macromolecules. Specifically, we focus on the use of molecular dynamics in NMR structural refinement, in understanding loop motion and catalytic activity of mutants in triose phosphate isomerase and in the application of free energy perturbation methods in protein design, site-specific mutagenesis and in thermal stability.