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Characterization of Transition States in Conformational Dynamics using Fuzzy Sets

Please always quote using this URN: urn:nbn:de:0297-zib-6791
  • Recently, a novel approach for the analysis of molecular dynamics on the basis of a transfer operator has been introduced. Therein conformations are considered to be disjoint metastable clusters within position space of a molecule. These clusters are defined by almost invariant characteristic functions that can be computed via {\em Perron Cluster} analysis. The present paper suggests to replace crisp clusters with {\em fuzzy} clusters, i.e. to replace characteristic functions with membership functions. This allows a more sufficient characterization of transiton states between different confor conformations and therefore leads to a better understanding of molecular dynamics. Fur thermore, an indicator for the uniqueness of metastable fuzzy clusters and a fast algorithm for the computation of these clusters are described. Numerical examples are included.

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Author:Marcus Weber, Tobias Galliat
Document Type:ZIB-Report
Tag:biochemical conformations; cluster analysis; conformational dynamics; fuzzy sets; molecular dynamics; transition states
MSC-Classification:03-XX MATHEMATICAL LOGIC AND FOUNDATIONS / 03Exx Set theory / 03E72 Fuzzy set theory
62-XX STATISTICS / 62Hxx Multivariate analysis [See also 60Exx] / 62H30 Classification and discrimination; cluster analysis [See also 68T10]
92-XX BIOLOGY AND OTHER NATURAL SCIENCES / 92-08 Computational methods
Date of first Publication:2002/03/15
Series (Serial Number):ZIB-Report (02-12)
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