title: DMG-α--a computational geometry library for multimolecular systems.
abstract: The DMG-α library grants researchers in the field of computational biology, chemistry, and biophysics access to an open-sourced, easy to use, and intuitive software for performing fine-grained geometric analysis of molecular systems. The library is capable of computing power diagrams (weighted Voronoi diagrams) in three dimensions with 3D periodic boundary conditions, computing approximate projective 2D Voronoi diagrams on arbitrarily defined surfaces, performing shape properties recognition using α-shape theory and can do exact Solvent Accessible Surface Area (SASA) computation. The software is written mainly as a template-based C++ library for greater performance, but a rich Python interface (pydmga) is provided as a convenient way to manipulate the DMG-α routines. To illustrate possible applications of the DMG-α library, we present results of sample analyses which allowed to determine nontrivial geometric properties of two Escherichia coli-specific lipids as emerging from molecular dynamics simulations of relevant model bilayers.
authors.affiliation: Faculty of Mathematics and Computer Science, ‡Malopolska Centre of Biotechnology, and §Faculty of Biochemistry, Biophysics and Biotechnology, Department of Computational Biophysics and Bioinformatics, Jagiellonian University , 31-007 Krakow, Poland.
authors.forename: Robert
authors.initials: R
authors.lastname: Szczelina
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Murzyn
mesh_terms: D055808:Drug Discovery / Q000379:methods*; D004926:Escherichia coli; D008051:Lipid Bilayers / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D012984:Software; D012997:Solvents / Q000737:chemistry; D014584:User-Computer Interface
chemical_list: D008051:Lipid Bilayers; D012997:Solvents