title: Azahar: a PyMOL plugin for construction, visualization and analysis of glycan molecules.
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 .
authors.affiliation: Instituto de Matemática Aplicada San Luis, IMASL, Universidad Nacional de San Luis and CONICET, D5700HHW, San Luis, Argentina. aarroyuelo@unsl.edu.ar.
authors.forename: Agustina
authors.identifier: 0000-0002-7249-755X
authors.initials: A
authors.lastname: Arroyuelo
authors.affiliation: Instituto de Matemática Aplicada San Luis, IMASL, Universidad Nacional de San Luis and CONICET, D5700HHW, San Luis, Argentina.
authors.forename: Jorge A
authors.initials: JA
authors.lastname: Vila
authors.affiliation: Instituto de Matemática Aplicada San Luis, IMASL, Universidad Nacional de San Luis and CONICET, D5700HHW, San Luis, Argentina. omarti@unsl.edu.ar.
authors.forename: Osvaldo A
authors.initials: OA
authors.lastname: Martin
mesh_terms: D002236:Carbohydrate Conformation; D008958:Models, Molecular; D009010:Monte Carlo Method; D011134:Polysaccharides / Q000737:chemistry*; D012984:Software
chemical_list: D011134:Polysaccharides
keywords: Glycans; Modelling; Structural bioinformatics