title: The impact of molecular dynamics on drug design: applications for the characterization of ligand-macromolecule complexes.
abstract: Among all tools available to design new drugs, molecular dynamics (MD) simulations have become an essential technique. Initially developed to investigate molecular models with a limited number of atoms, computers now enable investigations of large macromolecular systems with a simulation time reaching the microsecond range. The reviewed articles cover four years of research to give an overview on the actual impact of MD on the current medicinal chemistry landscape with a particular emphasis on studies of ligand-protein interactions. With a special focus on studies combining computational approaches with data gained from other techniques, this review shows how deeply embedded MD simulations are in drug design strategies and articulates what the future of this technique could be.
authors.affiliation: Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany. Electronic address: jeremie.mortier@fu-berlin.de.
authors.forename: Jérémie
authors.initials: J
authors.lastname: Mortier
authors.affiliation: Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany.
authors.forename: Christin
authors.initials: C
authors.lastname: Rakers
authors.affiliation: Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany.
authors.forename: Marcel
authors.initials: M
authors.lastname: Bermudez
authors.affiliation: Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany.
authors.forename: Manuela S
authors.initials: MS
authors.lastname: Murgueitio
authors.affiliation: Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland.
authors.forename: Sereina
authors.initials: S
authors.lastname: Riniker
authors.affiliation: Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany. Electronic address: gerhard.wolber@fu-berlin.de.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Wolber
mesh_terms: D000818:Animals; D001665:Binding Sites; D015195:Drug Design; D006801:Humans; D008024:Ligands; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D058990:Molecular Targeted Therapy; D004364:Pharmaceutical Preparations / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D015398:Signal Transduction / Q000187:drug effects; D013329:Structure-Activity Relationship
chemical_list: D008024:Ligands; D004364:Pharmaceutical Preparations; D011506:Proteins