Lukat G, Sommer B, Krüger J. Membrane simulation analysis using Voronoi tessellation (Conference Abstract). In:  Journal of Cheminformatics. Journal of Cheminformatics. Vol 6. Springer Science and Business Media LLC;  2014

Krüger, Jens

Lukat, Gunther

Sommer, Björn

Journal of Cheminformatics

English

PubMed

Gunther Lukat

Björn Sommer

Jens Krüger

Springer - Publisher Connector

ORAL PRESENTATION Open Access
Membrane simulation analysis using Voronoi
tessellation
Gunther Lukat1,2*, Björn Sommer1, Jens Krüger3
From 9th German Conference on Chemoinformatics
Fulda, Germany. 10-12 November 2013
The study of membranes and embedded proteins repre-
sents an advanced task in the field of molecular simula-
tion. While nowadays a profound selection of sampling
techniques, molecular topologies and theoretical
approaches is available, the analysis of actual simulation
data remains a difficult endeavour.
For homogeneous lipid bilayer simulations, the calcula-
tion of the bilayer thickness or area per lipid is directly
accessible. For lipid mixtures, e.g. with cholesterol or
embedded proteins, this is no longer the case. To face this
challenge, APL@Voro has been developed [1]. The open-
source and freely available graphical application is able to
handle united-atom and coarse-grained trajectories gener-
ated with GROMACS [2]. Instructive, two-dimensional
geometric representations of the lipid bilayer can easily be
created based on Voronoi diagrams and Delaunay triangu-
lations. The values, calculated on the geometric structures
can be visualized in an interactive environment, plotted
and exported to different file types (see Figure 1).
Even phase transitions within a bilayer can be tracked
and visualised in an instructive and convenient way.
APL@Voro represents a major improvement for the
analysis of complex membrane simulations. The applica-
tion is available at http://www.aplvoro.org.
* Correspondence: gunther@CELLmicrocosmos.org
1Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, NRW,
33615, Germany
Full list of author information is available at the end of the article
Figure 1 Pentamere of Vpu from HIV-1 in a POPC Bilayer. The Voronoi cells for the monomeres are colored, the cells for the lipids are left in
white.
Lukat et al. Journal of Cheminformatics 2014, 6(Suppl 1):O23
http://www.jcheminf.com/content/6/S1/O23
© 2014 Lukat et al; licensee Chemistry Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://
creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Authors’ details
1Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, NRW,
33615, Germany. 2Theoretical Astrophysics Group, Hamburg Observatory,
Hamburg, HH, 21029, Germany. 3Applied Bioinformatics, University of
Tübingen, Tübingen, BW, 72076, Germany.
Published: 11 March 2014
References
1. Lukat G, Krüger J, Sommer B: APL@Voro: A Voronoi-based Membrane
Analysis Tool for Gromacs Trajectories. J Chem Inf Model 2013, submitted.
2. Hess B, Kutzner C, van der Spoel D, Lindahl E: Gromacs 4: Algorithms for
Highly Efficient, Load-balanced, and Scalable Molecular Simulation.
J Chem Theory Comput 2008, 4:435-447.
doi:10.1186/1758-2946-6-S1-O23
Cite this article as: Lukat et al.: Membrane simulation analysis using
Voronoi tessellation. Journal of Cheminformatics 2014 6(Suppl 1):O23.
Open access provides opportunities to our 
colleagues in other parts of the globe, by allowing 
anyone to view the content free of charge.
Publish with ChemistryCentral and every
scientist can read your work free of charge
W. Jeffery Hurst, The Hershey Company.
available free of charge to the entire scientific community
peer reviewed and published immediately upon acceptance
cited in PubMed and archived on PubMed Central
yours     you keep the copyright
Submit your manuscript here:
http://www.chemistrycentral.com/manuscript/
Lukat et al. Journal of Cheminformatics 2014, 6(Suppl 1):O23
http://www.jcheminf.com/content/6/S1/O23
Page 2 of 2


Membrane simulation analysis using Voronoi tessellation

Publications at Bielefeld University

ORAL PRESENTATION Open AccessMembrane simulation analysis using VoronoitessellationGunther Lukat1,2*, Björn Sommer1, Jens Krüger3From 9th German Conference on ChemoinformaticsFulda, Germany. 10-12 November 2013The study of membranes and embedded proteins repre-sents an advanced task in the field of molecular simula-tion. While nowadays a profound selection of samplingtechniques, molecular topologies and theoreticalapproaches is available, the analysis of actual simulationdata remains a difficult endeavour.For homogeneous lipid bilayer simulations, the calcula-tion of the bilayer thickness or area per lipid is directlyaccessible. For lipid mixtures, e.g. with cholesterol orembedded proteins, this is no longer the case. To face thischallenge, APL@Voro has been developed [1]. The open-source and freely available graphical application is able tohandle united-atom and coarse-grained trajectories gener-ated with GROMACS [2]. Instructive, two-dimensionalgeometric representations of the lipid bilayer can easily becreated based on Voronoi diagrams and Delaunay triangu-lations. The values, calculated on the geometric structurescan be visualized in an interactive environment, plottedand exported to different file types (see Figure 1).Even phase transitions within a bilayer can be trackedand visualised in an instructive and convenient way.APL@Voro represents a major improvement for theanalysis of complex membrane simulations. The applica-tion is available at http://www.aplvoro.org.* Correspondence: gunther@CELLmicrocosmos.org1Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, NRW,33615, GermanyFull list of author information is available at the end of the articleFigure 1 Pentamere of Vpu from HIV-1 in a POPC Bilayer. The Voronoi cells for the monomeres are colored, the cells for the lipids are left inwhite.Lukat et al. Journal of Cheminformatics 2014, 6(Suppl 1):O23http://www.jcheminf.com/content/6/S1/O23© 2014 Lukat et al; licensee Chemistry Central Ltd. This is an Open Access article distributed under the terms of the Creative CommonsAttribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction inany medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Authors’ details1Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, NRW,33615, Germany. 2Theoretical Astrophysics Group, Hamburg Observatory,Hamburg, HH, 21029, Germany. 3Applied Bioinformatics, University ofTübingen, Tübingen, BW, 72076, Germany.Published: 11 March 2014References1. Lukat G, Krüger J, Sommer B: APL@Voro: A Voronoi-based MembraneAnalysis Tool for Gromacs Trajectories. J Chem Inf Model 2013, submitted.2. Hess B, Kutzner C, van der Spoel D, Lindahl E: Gromacs 4: Algorithms forHighly Efficient, Load-balanced, and Scalable Molecular Simulation.J Chem Theory Comput 2008, 4:435-447.doi:10.1186/1758-2946-6-S1-O23Cite this article as: Lukat et al.: Membrane simulation analysis usingVoronoi tessellation. Journal of Cheminformatics 2014 6(Suppl 1):O23.Open access provides opportunities to our colleagues in other parts of the globe, by allowing anyone to view the content free of charge.Publish with ChemistryCentral and everyscientist can read your work free of chargeW. Jeffery Hurst, The Hershey Company.available free of charge to the entire scientific communitypeer reviewed and published immediately upon acceptancecited in PubMed and archived on PubMed Centralyours     you keep the copyrightSubmit your manuscript here:http://www.chemistrycentral.com/manuscript/Lukat et al. Journal of Cheminformatics 2014, 6(Suppl 1):O23http://www.jcheminf.com/content/6/S1/O23Page 2 of 2

Membrane simulation analysis using Voronoi tessellation (Conference Abstract)

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Membrane simulation analysis using Voronoi tessellation (Conference Abstract)

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