The understanding of biochemical processes requires the study of structure and dynamics of biomolecules of varying size. In these investigations vast amounts of data are generated both in experiments and in numerical simulations. An interplay between chemical classification, mathematical data reduction and graphical data representation is necessary to aid in uncovering the essential structure of biomolecular processes and making them understandable to the human observer. The aim of this project is to develop a software environment which integrates molecular dynamics simulation, visualization, and analysis.

Publications

2023
Enhancing molecular visualization: Perceptual evaluation of line variables with application to uncertainty visualization Computers & Graphics, Vol.114, pp. 401-413, 2023 Anna Sterzik, Nils Lichtenberg, Michael Krone, Daniel Baum, Douglas W. Cunningham, Kai Lawonn BibTeX
DOI
Molecular Visualization
2016
ORBKIT – A modular Python toolbox for cross-platform post-processing of quantum chemical wavefunction data Journal of Computational Chemistry, 37(16), pp. 1511-1520, 2016 Gunter Hermann, Vincent Pohl, Jean Christophe Tremblay, Beate Paulus, Hans-Christian Hege, Axel Schild BibTeX
DOI
Molecular Visualization
2008
Analysis and Visualization of Molecular Conformations Doctoral thesis, Freie Universität Berlin, Fachbereich Mathematik und Informatik (P. Deuflhard), Der Andere Verlag, Tönning, 2008 Johannes Schmidt-Ehrenberg BibTeX
Molecular Visualization
2007
A Point-Based Algorithm for Multiple 3D Surface Alignment of Drug-Sized Molecules Doctoral thesis, Freie Universität Berlin, Peter Deuflhard, Joachim Selbig (Advisors), 2007 Daniel Baum PDF
BibTeX
URN
Molecular Visualization
2006
A Point-matching based algorithm for 3D surface alignment of drug-sized molecules Computational Life Sciences II, Second International Symposium, CompLife 2006, Cambridge (UK), Sept. 2006, pp. 183-193, Vol.4216, Lecture Notes in Bioinformatics, 2006 Daniel Baum, Hans-Christian Hege BibTeX
DOI
Molecular Visualization
Set-oriented dimension reduction: Localizing principal component analysis via hidden Markov models Computational Life Sciences II, Vol.4216, pp. 98-115, Springer, 2006 Illia Horenko, Johannes Schmidt-Ehrenberg, Christof Schütte BibTeX
Molecular Visualization
2005
Multiple semi-flexible 3D superposition of drug-sized molecules Computational Life Sciences: First International Symposium, CompLife 2005, pp. 198-207, Vol.3695, Lecture Notes on Computer Science, 2005 (preprint available as ) Daniel Baum BibTeX
DOI
Molecular Visualization
2003
Rigid body docking for Virtual Screening ZIB-Report 03-47 Andreas May, Steffen Eisenhardt, Johannes Schmidt-Ehrenberg, Frank Cordes PDF
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Molecular Visualization
2002
Metastable Conformations via successive Perron-Cluster Cluster Analysis of dihedrals ZIB-Report 02-40 Frank Cordes, Marcus Weber, Johannes Schmidt-Ehrenberg PDF
BibTeX
URN
Molecular Visualization
Visualizing Dynamic Molecular Conformations Proceedings of IEEE Visualization 2002, Robert J. Moorhead, Markus Gross, Kenneth I. Joy (Eds.), pp. 235-242, 2002 Johannes Schmidt-Ehrenberg, Daniel Baum, Hans-Christian Hege BibTeX
DOI
Molecular Visualization
2001
Visually stunning - Molecular conformations The Biochemist, 23(5), pp. 22-26, 2001 Johannes Schmidt-Ehrenberg, Daniel Baum, Hans-Christian Hege BibTeX
Molecular Visualization