APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories

Lukat G, Krueger J, Sommer B (2013)
Journal Of Chemical Information And Modeling 53(11): 2908-2925.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Abstract / Bemerkung
APL@Voro is a new program developed to aid in the analysis of GROMACS trajectories of lipid bilayer simulations. It can read a GROMACS trajectory file, a PDB coordinate file, and a GROMACS index file to create a two-dimensional geometric representation of a bilayer. Voronoi diagrams and Delaunay triangulations-generated for different selection models of lipids-support the analysis of the bilayer. The values calculated on the geometric structures can be visualized in a user-friendly interactive environment and, then, plotted and exported to different file types. APL@Voro supports complex bilayers with a mix of various lipids and proteins. For the calculation of the projected area per lipid, a modification of the well-known Voronoi approach is presented as well as the presentation of a new approach for including atoms into an existing triangulation. The application of the developed software is discussed for three example systems simulated with GROMACS. The program is written in C++, is open source, and is available free of charge.
Erscheinungsjahr
Zeitschriftentitel
Journal Of Chemical Information And Modeling
Band
53
Zeitschriftennummer
11
Seite
2908-2925
ISSN
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Lukat G, Krueger J, Sommer B. APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories. Journal Of Chemical Information And Modeling. 2013;53(11):2908-2925.
Lukat, G., Krueger, J., & Sommer, B. (2013). APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories. Journal Of Chemical Information And Modeling, 53(11), 2908-2925. doi:10.1021/ci400172g
Lukat, G., Krueger, J., and Sommer, B. (2013). APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories. Journal Of Chemical Information And Modeling 53, 2908-2925.
Lukat, G., Krueger, J., & Sommer, B., 2013. APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories. Journal Of Chemical Information And Modeling, 53(11), p 2908-2925.
G. Lukat, J. Krueger, and B. Sommer, “APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories”, Journal Of Chemical Information And Modeling, vol. 53, 2013, pp. 2908-2925.
Lukat, G., Krueger, J., Sommer, B.: APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories. Journal Of Chemical Information And Modeling. 53, 2908-2925 (2013).
Lukat, Gunther, Krueger, Jens, and Sommer, Björn. “APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories”. Journal Of Chemical Information And Modeling 53.11 (2013): 2908-2925.

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