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Biomolecular Modeling: Goals, Problems, Perspectives

Authors

  • Wilfred F. van Gunsteren Prof. Dr.,

    1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland, Fax: (+41) 44-632-1039
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  • Dirk Bakowies Dr.,

    1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland, Fax: (+41) 44-632-1039
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  • Riccardo Baron,

    1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland, Fax: (+41) 44-632-1039
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  • Indira Chandrasekhar Dr.,

    1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland, Fax: (+41) 44-632-1039
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  • Markus Christen,

    1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland, Fax: (+41) 44-632-1039
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  • Xavier Daura Prof. Dr.,

    1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland, Fax: (+41) 44-632-1039
    2. ICREA, Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
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  • Peter Gee Dr.,

    1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland, Fax: (+41) 44-632-1039
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  • Daan P. Geerke,

    1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland, Fax: (+41) 44-632-1039
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  • Alice Glättli Dr.,

    1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland, Fax: (+41) 44-632-1039
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  • Philippe H. Hünenberger Dr.,

    1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland, Fax: (+41) 44-632-1039
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  • Mika A. Kastenholz,

    1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland, Fax: (+41) 44-632-1039
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  • Chris Oostenbrink Dr.,

    1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland, Fax: (+41) 44-632-1039
    2. Pharmaceutical Sciences/Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083 P262, 1081 HV Amsterdam, The Netherlands
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  • Merijn Schenk Dr.,

    1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland, Fax: (+41) 44-632-1039
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  • Daniel Trzesniak,

    1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland, Fax: (+41) 44-632-1039
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  • Nico F. A. van der Vegt Dr.,

    1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland, Fax: (+41) 44-632-1039
    2. Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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  • Haibo B. Yu Dr.

    1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland, Fax: (+41) 44-632-1039
    2. Department of Chemistry, University of Wisconsin, 1101 University Ave, Madison, WI 53706, USA
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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.

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