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From Molecular Dynamics to Conformational Dynamics in Drug Design

Please always quote using this URN: urn:nbn:de:0297-zib-6878
  • Computational drug design studies molecular recognition in the {\em virtual lab}. The arising Hamiltonian dynamics is known to be chaotic and ill-conditioned already after picoseconds, whereas times are $msec$ up to $min$. Classical molecular dynamics with long term trajectory computation gives, at best, information about time and statistical ensemble averages. The present paper surveys a recent new modeling approach called {\em conformational dynamics}, which is due to the author and Ch. Schütte. This approach achieves information about the dy time scales by telescoping a short term deterministic model with a statistical model. Examples of small biomolecules are included.

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Metadaten
Author:Peter Deuflhard
Document Type:ZIB-Report
Tag:Hamiltonian dynamics; Markov chain; Perro; almost invariant sets; conformational dynamics; drug design; molecular dynamics; transition operator
MSC-Classification:62-XX STATISTICS / 62Pxx Applications [See also 90-XX, 91-XX, 92-XX] / 62P10 Applications to biology and medical sciences
65-XX NUMERICAL ANALYSIS / 65Cxx Probabilistic methods, simulation and stochastic differential equations (For theoretical aspects, see 68U20 and 60H35) / 65C05 Monte Carlo methods
65-XX NUMERICAL ANALYSIS / 65Fxx Numerical linear algebra / 65F15 Eigenvalues, eigenvectors
65-XX NUMERICAL ANALYSIS / 65Lxx Ordinary differential equations / 65L05 Initial value problems
65-XX NUMERICAL ANALYSIS / 65Lxx Ordinary differential equations / 65L08 Improperly posed problems
Date of first Publication:2002/04/11
Series (Serial Number):ZIB-Report (02-20)
ZIB-Reportnumber:02-20
Published in:Appeared in: M. Kirkilionis, S. Krömker, R. Rannacher, F. Toni (eds.) Trends in Nonlinear Analysis. Springer 2003, pp. 269-288
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