Overview Statistic: PDF-Downloads (blue) and Frontdoor-Views (gray)
The search result changed since you submitted your search request. Documents might be displayed in a different sort order.
  • search hit 10 of 406
Back to Result List

Visualizing conformations in molecular dynamics

Please always quote using this URN: urn:nbn:de:0297-zib-3859
  • The Monte Carlo simulation of the dynamics of complex molecules produces trajectories with a large number of different configurations to sample configuration space. It is expected that these configurations can be classified into a small number of conformations representing essential changes in the shape of the molecule. We present a method to visualize these conformations by point sets in the plane based on a geometrical distance measure between individual configurations. It turns out that different conformations appear as well-separated point sets. The method is further improved by performing a cluster analysis of the data set. The point-cluster representation is used to control a three-dimensional molecule viewer application to show individual configurations and conformational changes. The extraction of essential coordinates and visualization of molecular shape is discussed.

Download full text files

Export metadata

Additional Services

Share in Twitter Search Google Scholar Statistics - number of accesses to the document
Metadaten
Author:Christoph Best, Hans-Christian HegeORCiDGND
Document Type:ZIB-Report
Tag:Cluster Analysis; Conformations; Molecular Dynamics; Visualization
MSC-Classification:62-XX STATISTICS / 62-07 Data analysis
92-XX BIOLOGY AND OTHER NATURAL SCIENCES / 92Cxx Physiological, cellular and medical topics / 92C40 Biochemistry, molecular biology
92-XX BIOLOGY AND OTHER NATURAL SCIENCES / 92Exx Chemistry (For biochemistry, see 92C40) / 92E10 Molecular structure (graph-theoretic methods, methods of differential topology, etc.)
PACS-Classification:00.00.00 GENERAL / 07.00.00 Instruments, apparatus, and components common to several branches of physics and astronomy (see also each subdiscipline for specialized instrumentation and techniques) / 07.05.-t Computers in experimental physics; Computers in education, see 01.50.H- and 01.50.Lc; Computational techniques, see 02.70.-c; Quantum computation architectures and implementations, see 03.67.Lx; Optical computers, see 42.79.Ta / 07.05.Rm Data presentation and visualization: algorithms and implementation
Date of first Publication:1998/12/30
Series (Serial Number):ZIB-Report (SC-98-42)
ZIB-Reportnumber:SC-98-42
Published in:A rev. vers. appeared under the title "Visualizing and Identifying Conformational Ensembles in Molecular Dynamics Trajectories" in: Computing in Science and Engineering 4 (3) May/June (2002), pp. 68-75
Accept ✔
Diese Webseite verwendet technisch erforderliche Session-Cookies. Durch die weitere Nutzung der Webseite stimmen Sie diesem zu. Unsere Datenschutzerklärung finden Sie hier.