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Biomolecular Modeling: Goals, Problems, Perspectives

2006; Wiley; Volume: 45; Issue: 25 Linguagem: Inglês

10.1002/anie.200502655

1521-3773

Wilfred F. van Gunsteren, Dirk Bakowies, Riccardo Baron, Indira Chandrasekhar, Markus Christen, Xavier Daura, Peter J. 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 Yu,

Enzyme Structure and Function

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.