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Keywords:

  • enhanced sampling;
  • molecular dynamics;
  • conformational change;
  • free energy;
  • DNA

Abstract

The behavior of proteins and DNA is largely determined by their dynamics, which involves transitions between various conformational states. Computer simulations can provide detailed insights into these dynamics, but the long-time scales of the transitions severely complicate such an approach. In this review, we present a few recently developed enhanced sampling techniques for the simulation of conformational changes at atomic resolution. To illustrate the application of these techniques, we discuss the isomerization of a nonprolyl peptide bond in a collagenase and a joint simulation-experimental study of a DNA-dye system. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2012