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

VILA, JORGE A.; ARROYUELO, AGUSTINA.; MARTÍN OSVALDO A.

Villa Gral. Belgrano

Congreso; GlycoAR 2016; 2016

There is an existing trend towards modelling complex molecular systems yet most of themolecular software packages are protein-centered [1]. Therefore, bioinformatics toolsoriented to glycobiology are rare or disperse [2]. This fact is not consistent with theevidence showing that glycoconjugates are involved in most disease processes like viralor bacterial infection, metastasis, autoimmunity or inflammation [3, 4], and thatglycosylation is the most abundant post-translational modification both in terms ofnumber of modified proteins and consequential molecular diversity [5]. Therefore, theunderstanding of glycan tertiary structure is tightly paired with the comprehension of theirbiological involvement. As with other molecules, like proteins, visualization of the 3Dstructures of glycans add valuable information for understanding their biological function.Hence, here we introduce Azahar, an environment for the creation, visualization andanalysis of glycan molecules. Azahar is implemented in Python and works as a plugin forthe well known PyMOL package [6]. Besides the already available visualization andanalysis options provided by PyMOL, Azahar includes 3 cartoon-like representations andtools for 3D structure caracterization such as a comformational search using a MonteCarlo with minimization routine and also tools to analyze single glycans ortrajectories/ensembles including radius of gyration, Ramachandran plots and hydrogenbonds. Azahar is freely available to install at http://www.pymolwiki.org/index.php/Azaharand the source code is available at https://github.com/agustinaarroyuelo/Azahar