Membrane simulation analysis using Voronoi tessellation - Springer Link
Lukat et al. Journal of Cheminformatics 2014, 6(Suppl 1):O23 http://www.jcheminf.com/content/6/S1/O23
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 represents an advanced task in the field of molecular simulation. 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 calculation 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 opensource and freely available graphical application is able to
handle united-atom and coarse-grained trajectories generated with GROMACS [2]. Instructive, two-dimensional geometric representations of the lipid bilayer can easily be created based on Voronoi diagrams and Delaunay triangulations. 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 application is available at http://www.aplvoro.org.
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.
* Correspondence: [email protected] 1 Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, NRW, 33615, Germany Full list of author information is available at the end of the article © 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.
Lukat et al. Journal of Cheminformatics 2014, 6(Suppl 1):O23 http://www.jcheminf.com/content/6/S1/O23
Page 2 of 2
Authors’ details 1 Bio-/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.
Publish with ChemistryCentral and every scientist can read your work free of charge Open access provides opportunities to our colleagues in other parts of the globe, by allowing anyone to view the content 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/
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 represents an advanced task in the field of molecular simulation. 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 calculation 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 opensource and freely available graphical application is able to
handle united-atom and coarse-grained trajectories generated with GROMACS [2]. Instructive, two-dimensional geometric representations of the lipid bilayer can easily be created based on Voronoi diagrams and Delaunay triangulations. 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 application is available at http://www.aplvoro.org.
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.
* Correspondence: [email protected] 1 Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, NRW, 33615, Germany Full list of author information is available at the end of the article © 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.
Lukat et al. Journal of Cheminformatics 2014, 6(Suppl 1):O23 http://www.jcheminf.com/content/6/S1/O23
Page 2 of 2
Authors’ details 1 Bio-/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.
Publish with ChemistryCentral and every scientist can read your work free of charge Open access provides opportunities to our colleagues in other parts of the globe, by allowing anyone to view the content 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/
