title: Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.
abstract: A historical perspective on the application of molecular dynamics (MD) to biological macromolecules is presented. Recent developments combining state-of-the-art force fields with continuum solvation calculations have allowed us to reach the fourth era of MD applications in which one can often derive both accurate structure and accurate relative free energies from molecular dynamics trajectories. We illustrate such applications on nucleic acid duplexes, RNA hairpins, protein folding trajectories, and protein-ligand, protein-protein, and protein-nucleic acid interactions.
authors: Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA.
authors: P A
authors: PA
authors: Kollman
authors: I
authors: I
authors: Massova
authors: C
authors: C
authors: Reyes
authors: B
authors: B
authors: Kuhn
authors: S
authors: S
authors: Huo
authors: L
authors: L
authors: Chong
authors: M
authors: M
authors: Lee
authors: T
authors: T
authors: Lee
authors: Y
authors: Y
authors: Duan
authors: W
authors: W
authors: Wang
authors: O
authors: O
authors: Donini
authors: P
authors: P
authors: Cieplak
authors: J
authors: J
authors: Srinivasan
authors: D A
authors: DA
authors: Case
authors: T E
authors: TE
authors: Cheatham
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry; D008958:Models, Molecular; D015394:Molecular Structure; D011506:Proteins / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D011506:Proteins; D012313:RNA; D004247:DNA