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Azahar: a PyMOL plugin for construction, visualization and analysis of glycan molecules

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Abstract

Glycans are key molecules in many physiological and pathological processes. As with other molecules, like proteins, visualization of the 3D structures of glycans adds valuable information for understanding their biological function. Hence, here we introduce Azahar, a computing environment for the creation, visualization and analysis of glycan molecules. Azahar is implemented in Python and works as a plugin for the well known PyMOL package (Schrodinger in The PyMOL molecular graphics system, version 1.3r1, 2010). Besides the already available visualization and analysis options provided by PyMOL, Azahar includes 3 cartoon-like representations and tools for 3D structure caracterization such as a comformational search using a Monte Carlo with minimization routine and also tools to analyse single glycans or trajectories/ensembles including the calculation of radius of gyration, Ramachandran plots and hydrogen bonds. Azahar is freely available to download from http://www.pymolwiki.org/index.php/Azahar and the source code is available at https://github.com/agustinaarroyuelo/Azahar.

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Acknowledgments

This work was supported by: A Warren L. DeLano Memorial PyMOL Open-Source Fellowship; PIP-0030 from CONICET-Argentina; and PICT-2014-0556 from ANPCyT-Argentina.

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Authors and Affiliations

  1. Instituto de Matemática Aplicada San Luis, IMASL, Universidad Nacional de San Luis and CONICET, D5700HHW, San Luis, Argentina

    Agustina Arroyuelo, Jorge A. Vila & Osvaldo A. Martin

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  1. Agustina Arroyuelo
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  2. Jorge A. Vila
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  3. Osvaldo A. Martin
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Correspondence to Agustina Arroyuelo or Osvaldo A. Martin.

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Arroyuelo, A., Vila, J.A. & Martin, O.A. Azahar: a PyMOL plugin for construction, visualization and analysis of glycan molecules. J Comput Aided Mol Des 30, 619–624 (2016). https://doi.org/10.1007/s10822-016-9944-x

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