• Data Base Content

    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.

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