The SugarBind Database (SugarBindDB) was created in 2002 as part of an effort by the MITRE Corporation (http://www.mitre.org) to develop a pathogen-capture technology based on the binding of viral, bacterial and biotoxin lectins to specific glycans (aka, sugars, carbohydrates) displayed on glycoprotein films. The database content results from compiling publicly available information. First an on-line literature search locates candidate articles published in peer-reviewed scientific journals. Then abstracts are screened for relevance, and articles that appear likely to contain information on the binding of a human pathogen to a specific glycan are acquired, printed, and marked for data extraction. Reviews are used to identify primary literature, but are generally not cited in the database. Fewer than 5% of information sources include textbooks and conference proceedings.
Only sugar sequences that demonstrate consistent binding to pathogen lectins are entered into SugarBindDB. In some cases, authors have identified a precise lectin binding site or “glycotope” within a larger carbohydrate structure, while in others an entire oligosaccharide is listed.
In 2010, the 2008 version of the database was migrated from MITRE Corporation to the SIB Swiss Institute of Bioinformatics in Geneva, Switzerland. From then, substantial changes in the database design and usage were undertaken and previous content was significantly extended.
The database can be queried by names of the different entities involved in the carbohydrate-protein interaction:
The database can also be queried by context such as the affected area in the pathology (e.g. intestine) or by published references. Finally, a sugar composition can be input as a query or a sugar structure can be drawn with GlycanBuilder (http://code.google.com/p/glycanbuilder/).
From each entry point accessed in the database, further information can be browsed. The biological context of each ligand is shown in relation to a disease, to other known ligands, to similar lectins, etc.
Note that the upper menu (grey) bar allows browsing the database from content lists.
The latest major update was performed on: February 21, 2018.
Please cite :
Mariethoz J, Khatib K, Alocci D, Campbell MP, Karlsson NG, Packer NH, Mullen EH, Lisacek F : SugarBindDB, a resource of glycan-mediated host-pathogen interactions Nucl. Acids Res. (04 January 2016) 44 (D1): D1243-D1250. doi: 10.1093/nar/gkv1247