Biomolecular modeling: Goals, problems, perspectives

Wilfred F. Van Gunsteren, Dirk Bakowies, Riccardo Baron, Indira Chandrasekhar, Markus Christen, Xavier Daura, Peter Gee, Daan P. Geerke, Alice Glättli, Philippe H. Hünenberger, Mika A. Kastenholz, Chris Oostenbrink, Merijn Schenk, Daniel Trzesniak, Nico F.A. Van Der Vegt, Haibo B. Yu

Research output: Contribution to journalReview articleResearchpeer-review

430 Citations (Scopus)


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. © 2006 Wiley-VCH Verlag GmbH & Co. KGaA.
Original languageEnglish
Pages (from-to)4064-4092
JournalAngewandte Chemie - International Edition
Issue number25
Publication statusPublished - 19 Jun 2006


  • Computer simulation
  • Force-field techniques
  • Molecular dynamics
  • Molecular modeling


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