• Data Base Content

    This is an annotated database that contains the 3D structural information of more than 120 entries of monosaccharides. These monosaccharides the alphabet of the building blocks of the vast majority of oligosaccharides, complex carbohydrates such as “glycan determinants” (blood group antigens, core structures, fucosylated oligosaccharides, sialylated oligosaccharides, Lewis antigens, GPI-anchors, N-and O- linked oligosaccharides, globosides,…), glycosaminoglycans, plants and, algal polysaccharides, as well as some bacterial polysaccharides.

    There exists several ways of encoding and representing glycans. While maintaining the spirit of using the symbolic representation for monosaccharides (and towards glycans) this set of rules provides the necessary extension to the construction of three-dimensional structures, allowing encoding for computational manipulation. A detailed description of these is available within the chaper entitled: “Symbolic Representation of Monosaccharides in the Age of Glycobiology” http://www.glycopedia.eu . It is possible to concatenate the symbolic representation of monosaccharides with a limited number of structural descriptors to achieve a fairly exhaustive and comprehensive nomenclature which can be further used in constructing three dimensional structures of glycans.

    This can be achieved using the following set

    Residue Letter Name: Rib, Ara, Xyl, Lyx, All, Alt, Glc, Man, Gul, Ido, Gal, Tal,….and abbreviated trivial name.

    [O-ester and ethers]: (when present) are shown attached to the symbol with a number, e.g.
    6Ac for 6-O-acetyl group
    3S for 3-O-sulfate group
    3P for 6-O-phosphate group
    6Me for 6-O-Methyl group
    36Anh for 3-6 Anhydro
    Pyr for Pyruvate

    Absolute Configuration: D or L The D-configuration for monosaccharide and the L configuration for Fucose and Idose are implicit and does not appear in the symbol. Otherwise the L configuration, is indicated in the symbol, as in the case of Arabinose or L Galactose.

    For those occurring in the furanose form, a letter N or S in inserted in the symbol, indicating the northern (N) or Southern (S) conformation of the five membered ring.

    Anomeric configuration: The nature of the glycosidic configuration (α or β) is explicitly set within the symbol.

    Ring conformation: All pyranoses in the D-configuration are assumed to have 4C1 chair conformation; those in the L configuration are assumed to have 1C4 chair conformation. Otherwise, the ring conformation is indicated in the symbol, as 2S0 in the case of α-L-Idopyranose. N or S indicates the conformation of the five membered rings on the conformational wheel.

    The following table gives the content of the data base as per September 2013.

    For establishing the 3D data base, they all have been subjected to systematic conformational sampling to determine their conformational preferences, using molecular mechanics optimization. Whereas most of the monosaccharides exhibit a fairly rigid ring conformation some cases exist such as in the case of iduronic acid, idose, and all furanosides where several ring shapes can occur. In these cases, the low energy conformations are available for each entry.

  • Data Query

    database is available from Glyco3D portal or directly from http://monosaccharide.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 monosaccharide name, its absolute configuration (D or L) its anomeric configuration, category and molecular weight to user to make an informed choice.

  • Advanced Search

    Four search boxes appear each 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.

  • 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, (when available the symbol notation for carbohydrates of the Consortium for Functional Glycomics http://www.functionalglycomics.org the molecular weight, Additional comments and literature references are present if available. The illustrative representations of the monosaccharide can be viewed through the “Zoombox” feature that allows the selected image to be zoomed and highlighted.

  • View and Download

    This tab incorporates the low energy conformation of the monosaccharide and its methyl glycoside. The molecules are displayed under Jmol applet windows that enable basic viewing and measurement options, under the right-click options. Each of the conformation can be downloaded from this section, the coordinate files being at the PDB format.

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