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      Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins.

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          Abstract

          Understanding how glycosylation affects protein structure, dynamics, and function is an emerging and challenging problem in biology. As a first step toward glycan modeling in the context of structural glycobiology, we have developed Glycan Reader and integrated it into the CHARMM-GUI, http://www.charmm-gui.org/input/glycan. Glycan Reader greatly simplifies the reading of PDB structure files containing glycans through (i) detection of carbohydrate molecules, (ii) automatic annotation of carbohydrates based on their three-dimensional structures, (iii) recognition of glycosidic linkages between carbohydrates as well as N-/O-glycosidic linkages to proteins, and (iv) generation of inputs for the biomolecular simulation program CHARMM with the proper glycosidic linkage setup. In addition, Glycan Reader is linked to other functional modules in CHARMM-GUI, allowing users to easily generate carbohydrate or glycoprotein molecular simulation systems in solution or membrane environments and visualize the electrostatic potential on glycoprotein surfaces. These tools are useful for studying the impact of glycosylation on protein structure and dynamics.

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          Author and article information

          Journal
          J Comput Chem
          Journal of computational chemistry
          1096-987X
          0192-8651
          Nov 15 2011
          : 32
          : 14
          Affiliations
          [1 ] Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas, USA.
          Article
          NIHMS308581
          10.1002/jcc.21886
          3188666
          21815173
          Copyright © 2011 Wiley Periodicals, Inc.

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