title: Biomolecular simulation: a computational microscope for molecular biology.
abstract: Molecular dynamics simulations capture the behavior of biological macromolecules in full atomic detail, but their computational demands, combined with the challenge of appropriately modeling the relevant physics, have historically restricted their length and accuracy. Dramatic recent improvements in achievable simulation speed and the underlying physical models have enabled atomic-level simulations on timescales as long as milliseconds that capture key biochemical processes such as protein folding, drug binding, membrane transport, and the conformational changes critical to protein function. Such simulation may serve as a computational microscope, revealing biomolecular mechanisms at spatial and temporal scales that are difficult to observe experimentally. We describe the rapidly evolving state of the art for atomic-level biomolecular simulation, illustrate the types of biological discoveries that can now be made through simulation, and discuss challenges motivating continued innovation in this field.
authors.affiliation: D. E. Shaw Research, New York, New York 10036, USA. Ron.Dror@DEShawResearch.com
authors.forename: Ron O
authors.initials: RO
authors.lastname: Dror
authors.forename: Robert M
authors.initials: RM
authors.lastname: Dirks
authors.forename: J P
authors.initials: JP
authors.lastname: Grossman
authors.forename: Huafeng
authors.initials: H
authors.lastname: Xu
authors.forename: David E
authors.initials: DE
authors.lastname: Shaw
mesh_terms: D000818:Animals; D001692:Biological Transport; D002462:Cell Membrane / Q000378:metabolism; D006801:Humans; D008958:Models, Molecular; D008967:Molecular Biology / Q000295:instrumentation / Q000379:methods*; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D011506:Proteins