title: Applications of Discrete Molecular Dynamics in biology and medicine.
abstract: Discrete Molecular Dynamics (DMD) is a physics-based simulation method using discrete energetic potentials rather than traditional continuous potentials, allowing microsecond time scale simulations of biomolecular systems to be performed on personal computers rather than supercomputers or specialized hardware. With the ongoing explosion in processing power even in personal computers, applications of DMD have similarly multiplied. In the past two years, researchers have used DMD to model structures of disease-implicated protein folding intermediates, study assembly of protein complexes, predict protein-protein binding conformations, engineer rescue mutations in disease-causative protein mutants, design a protein conformational switch to control cell signaling, and describe the behavior of polymeric dispersants for environmental cleanup of oil spills, among other innovative applications.
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, United States. Electronic address: eproctor@mit.edu.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Proctor
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, United States. Electronic address: dokh@unc.edu.
authors.forename: Nikolay V
authors.initials: NV
authors.lastname: Dokholyan
mesh_terms: D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D015202:Protein Engineering; D017510:Protein Folding; D012313:RNA / Q000737:chemistry
chemical_list: D012313:RNA