Role of Molecular Dynamics and Related Methods in Drug Discovery

Molecular dynamics (MD) and related methods are close to becoming routine computational tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and entropic effects. This allows a more accurate estimate of the thermodynamics and kinetics associated with drug-target recognition and binding, as better algorithms and hardware architectures increase their use. Here, we review the theoretical background of MD and enhanced sampling methods, focusing on free-energy perturbation, metadynamics, steered MD, and other methods most consistently used to study drug-target binding. We discuss unbiased MD simulations that nowadays allow the observation of unsupervised ligand-target…

• MD
  Ministero dell’Istruzione, dell’Università e della Ricerca
• AI
  Associazione Italiana per la Ricerca sul Cancro

  Award: 14140
• UD
  Università di Bologna
• II
  Istituto Italiano di Tecnologia