BiOligo is an annotated database that contains the 3D structural information
of more than 250 entries of bioactive oligosaccharides (referred to as
“glycan determinants”). The glycan determinants
are complex carbohydrates with their associated substitutions and aglycones
that are recognized by glycan-binding proteins; these include lectins,
receptors, toxins, microbial adhesins, antibodies, and enzymes (2). They
belong to the widely-occurring families like the blood group antigens,
core structures, fucosylated oligosaccharides, sialylated oligosaccharides,
Lewis antigens, GPI-anchors, N-linked oligosaccharides, globosides,….).
For establishing the 3D data base, they all have been subjected to systematic
conformational sampling to determine their conformational preferences,
using the Shape software. Several low energy conformations (1 to 5)
are available for each entry. The details concerning the construction
of the BiOligo database are given in Note 1.
Data Query
The database is available from Glyco3D portal or directly from
http://bioligo.cermav.cnrs.fr.
Upon reaching the search page, two buttons to query the data base appear
on the left hand panel: Simple search and Advanced search.
Simple Search
A search box is provided, in which the user inputs textual information
related to the search. The result is a prompt to guide the user in
selecting from the “hits” found in the data base, by a simple search engine.
A preview of the results is displayed in an accordion fashion. This can be
used to expand or minimize the preview of the listed results of the user
query for a first glance into the entries matching the request to the database.
The preview provides the glycan name, category and molecular weight to user
to make an informed choice.
Advanced Search
Four search boxes appear each of them of them offering the choice
between criteria to select: Trivial name; type of constituent,
category, molecular weight. A slider is provided for assigning a range
of values to be queried in the molecular weight of the data base entries.
It consists of two cursors that can navigate on a bar for specifying
the minimum and maximum limit of the search. Two text fields display
the values of the current position on the slider bar. The slider cursors
auto-adjust themselves when values are entered directly in the text boxes.
The “auto complete” function
Both the Simple Search and the Advanced Search options are equipped
with an “auto-complete” function, which guides the user while querying
the database. It comprises two parts; (i) a single filed of entered text:
(ii) the auto-prompt when the data is entered, through which the desired
hit in the data base can be selected either by scrolling down with the mouse,
or by using the arrow keys on the keyboard.
Results
The detailed results are organized under two tabs: “Molecule Information” and “View and Download”.
Molecule Information
This includes the trivial name of the glycan, its sequence, the graphical representation
of the stereo-chemical configuration, the symbol notation for carbohydrates
of the Consortium for Functional Glycomics, the molecular weight, the glycan category
or family in which it has been classified in the BiOligo Database,
the glycan composition (i.e. the comprising glycan type and number
of each such glycan) and the glycosidic linkages present in it.
Additional comments and literature references are present if available.
The illustrative representations of the glycan can be viewed through
the “Zoombox” feature that allows the selected image to be zoomed and highlighted.
View and Download
This tab incorporates the best representatives of the families of the most-probable
low energy conformations. The molecules are displayed under Jmol applet windows
that enable basic viewing and measurement options, under the right-clik options.
Each of the conformation can be downloaded from this section, the coordinate
files being at the PDB format.