Glyconvert – The Portal for Conversion Glycoinformatics Formats to General-Purpose Molecular Formats

Carbohydrates are important biomolecules which play a significant role in cell-cell recognition and other key biological processes. Thanks to high-performance structure determination methods, we have nowadays available a huge amount of biomolecular structures (including saccharides). The glycoinformatics databases are essential for storing specific knowledge about glycans because general-purpose databases do not have enough capacity and resources for preservation all the interesting information. These structures are archived in databases such as Unicarb-DB [1] and Glyconnect [2], where their structures are stored in GlycoCT format [3], which was developed for description of saccharide molecules. The GlycoCT format is useful mainly in machine processing and can be easily generated from the SNFG symbolic representation by SugarSketcher [4], but it is not easy to read by humans. Other structural formats are more appropriate for human processing, e.g. the modified IUPAC condensed in linear form; however, the representation of a molecule in this format may not be unique.

An important challenge of current glycobioinformatics is to combine the advantages of the human-readable and machine-readable format. In this work we address this challenge by implementing a tool for translation between these two formats. Additionally, we want to allow translation into general-purpose structural molecular formats such as InChI, InChIKey, SMILES. This will enable simple searches in common databases that can contain interesting and useful glycan information, e.g. CFG, PubChem [5], ChEBI [6].