title: Biomolecular modeling: Goals, problems, perspectives.
abstract: Computation based on molecular models is playing an increasingly important role in biology, biological chemistry, and biophysics. Since only a very limited number of properties of biomolecular systems is actually accessible to measurement by experimental means, computer simulation can complement experiment by providing not only averages, but also distributions and time series of any definable quantity, for example, conformational distributions or interactions between parts of systems. Present day biomolecular modeling is limited in its application by four main problems: 1) the force-field problem, 2) the search (sampling) problem, 3) the ensemble (sampling) problem, and 4) the experimental problem. These four problems are discussed and illustrated by practical examples. Perspectives are also outlined for pushing forward the limitations of biomolecular modeling.
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland. wfvgn@igc.phys.chem.ethz.ch
authors.forename: Wilfred F
authors.initials: WF
authors.lastname: van Gunsteren
authors.forename: Dirk
authors.initials: D
authors.lastname: Bakowies
authors.forename: Riccardo
authors.initials: R
authors.lastname: Baron
authors.forename: Indira
authors.initials: I
authors.lastname: Chandrasekhar
authors.forename: Markus
authors.initials: M
authors.lastname: Christen
authors.forename: Xavier
authors.initials: X
authors.lastname: Daura
authors.forename: Peter
authors.initials: P
authors.lastname: Gee
authors.forename: Daan P
authors.initials: DP
authors.lastname: Geerke
authors.forename: Alice
authors.initials: A
authors.lastname: Glättli
authors.forename: Philippe H
authors.initials: PH
authors.lastname: Hünenberger
authors.forename: Mika A
authors.initials: MA
authors.lastname: Kastenholz
authors.forename: Chris
authors.initials: C
authors.lastname: Oostenbrink
authors.forename: Merijn
authors.initials: M
authors.lastname: Schenk
authors.forename: Daniel
authors.initials: D
authors.lastname: Trzesniak
authors.forename: Nico F A
authors.initials: NF
authors.lastname: van der Vegt
authors.forename: Haibo B
authors.initials: HB
authors.lastname: Yu
mesh_terms: D003198:Computer Simulation; D008954:Models, Biological; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins