Connection of saccharide database UnicarbKb with common databases of molecular structures

SUCHÁNKOVÁ, Pavla and Radka SVOBODOVÁ VAŘEKOVÁ. Connection of saccharide database UnicarbKb with common databases of molecular structures. In XVIII. setkání biochemiků a molekulárních biologů, 2017. 2017. ISBN 978-80-210-8765-1.

Basic information

• Original name: Connection of saccharide database UnicarbKb with common databases of molecular structures
• Authors: SUCHÁNKOVÁ, Pavla (203 Czech Republic, guarantor, belonging to the institution) and Radka SVOBODOVÁ VAŘEKOVÁ (203 Czech Republic, belonging to the institution).
• Edition: XVIII. setkání biochemiků a molekulárních biologů, 2017, 2017.

Other information

• Original language: English
• Type of outcome: Conference abstract
• Field of Study: 10201 Computer sciences, information science, bioinformatics
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• RIV identification code: RIV/00216224:14740/17:00108802
• Organization unit: Central European Institute of Technology
• ISBN: 978-80-210-8765-1
• Keywords in English: glycan; GlycoCT; InChI; InChIKey; PDB; PubChem; UnicarbKB
• Tags: rivok

Abstract

Carbohydrates are important biomolecules, which play 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). These structures are archived in UnicarbKb [1] database, where they are stored in GlycoCT format [2] which was developed for describing of saccharide molecule. An important challenge of current glycobioinformatics is a connection of UnicarbKb with common databases of molecular structures (e.g., Pubchem [3]). We focused on this topic and developed a workflow for translation of GlycoCT format to SMILES and Inchi. Based on these standard formats, we established a linkage between Unicarb and Pubchem databases. We will present the workflow and also information describing a matching between these databases.

Links

• LQ1601, research and development project: Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR