title: Discovery through the computational microscope.
abstract: All-atom molecular dynamics simulations have become increasingly popular as a tool to investigate protein function and dynamics. However, researchers are concerned about the short time scales covered by simulations, the apparent impossibility to model large and integral biomolecular systems, and the actual predictive power of the molecular dynamics methodology. Here we review simulations that were in the past both hotly disputed and considered key successes, namely of proteins with mainly mechanical functions (titin, fibrinogen, ankyrin, and cadherin). The simulation work covered shows how state-of-the-art modeling alleviates some of the prior concerns and how unrefuted discoveries are made through the "computational microscope."
authors.affiliation: Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Eric H
authors.initials: EH
authors.lastname: Lee
authors.forename: Jen
authors.initials: J
authors.lastname: Hsin
authors.forename: Marcos
authors.initials: M
authors.lastname: Sotomayor
authors.forename: Gemma
authors.initials: G
authors.lastname: Comellas
authors.forename: Klaus
authors.initials: K
authors.lastname: Schulten
mesh_terms: D000818:Animals; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins