Publications on Glycobioinformatics

on the January 31, 2019

In the framework of Glyco@Alps WP4, important advances have been performed to provide the international community with glyco-related databases. Four publications deal with three new databases developed thanks to national and international collaborations (DTU, ICBMS and SIB).
In the framework of Glyco@Alps WP4 “Enabling Glycotechnologies”, four publications deal with three new databases developed thanks to national and international collaborations (Danish University Technology-Copenhague ; Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Lyon ; Swiss Institute Bioinformatics, Genève). The partnership with ICBMS and SIB is in the framework of the Alliance Campus Rhodanien in which Univ. Grenoble Alpes participates. 

These databases were built according to the FAIR (Findable, Accessible, Interoperable, and Re-usable) principles in the extension of the Glyco3D portals and MatrixDB.

François Bonnardel, Glyco@Alps PhD student, works on UniLectin3D. A classification of lectins according to their 3D structures and the ligands with which they interact gives this curated database many perspectives of analysis, understanding and prediction. UniLectin3D replaces lectins component of the glyco3D portal and offer numerous links to other databases: UniProt for proteins, PLIP for interactions, PDB Care for sugar structure validation (doi: 10.1093 / nar / gky832). 
EPS-DB is a web database dedicated to bacterial exopolysaccharides (EPS). Its originality is to cover structures and functional properties. Each EPS is characterized by its different levels of structure, taxonomy, growth conditions and strains extraction, functional properties as well as interacting proteins. The use of standard nomenclature and representation ensures interoperability with major domain databases (doi: 10.1016/j.carbpol.2018.10.063).

MatrixDB is a database of biomolecular interactions focused in particular on the interactions between extracellular matrix proteins and glycosaminoglycans (GAGs) such as heparin / heparan sulfate, hyaluronic acid, dermatan, chondroitin and keratan sulfate. MatrixDB has new features that now allow the generation of 3D structures from a GAG sequence. This feature is part of a pipeline that converts GAG sequences into standardized formats (IUPAC, SNFG, and GlycoCT) available in MatrixDB and then generates 3D models in PDB format that is compatible with most graphics software (PyMol, VMD, SweetUnityMol, ...) (doi: 10.1093 / ny / gky1035 and 10.1093 / glycob / cwy084).

Published on January 31, 2019