• Data Base Content

    Antibodies are glycoproteins belonging to the immunoglobulin superfamily. Three-dimensional structures have been established from x-ray crystallography as listed in http://www.bioinf.org.uk/abs/sacs/. Anti-carbohydrate antibodies with specificity to oligosaccharides and polysaccharides are of a high importance in immunology and vaccine development (1). The present data base is concerned with the limited set of high resolution structures of carbohydrate-antibody complexes. Analysis of these complexes reveals general trends about how antibodies recognize different types of carbohydrates. Antibodies which recognize a terminal carbohydrate motif generally feature cavity-like binding sites, where one or more carbohydrate residues are anchored in the cavity by “end-on” extension. Antibodies which recognize an internal carbohydrate motif, as a single repeat of a bacterial polysaccharide for example) generally exhibit groove-like binding sites, or very large cavities which are open at both ends of the site, allowing for “side-on” entry of the antigen.
  • Data Query

    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 right click opens a window on “Antibody information”.
  • Advanced Search

    Under the name “Select Criteria” a search box offers to select among the following items:
    1. nomenclature
    2. antibodyoriginimmunoglobulin type
    A search box is provided in which appears a drop-down button enlisting all the entries corresponding to the selected item. The result is prompt to guide the user in selecting the “hits” found in the data base, by a simple search engine.
    More complex search can be made by combining criteria which can be combined from up to four search boxes. A preview of the results is displayed. The amount of information provided allows the user to make an informed choice prior going to “Antibody Information”.
  • Results

    The detailed results are available under two tabs: “Antibody Information” and “Display and Download”.
  • Antibody Information

    Under the button: “Antibody Information” are given: origin, name of the antibody, nomenclature of the bound carbohydrate, PDB code, resolution, comment, immunoglobulin class, reference to the original article. Provision is also given to view a still three-dimensional ribbon type representation of the three-dimensional structure.
    Links to Medline (www.ncbi.nlm.nih.gov/pubmed) and Protein Data Base (www.rcsb.org) are also provided.
  • Display and Download

    On this page, is given a three-dimensional representation of the three-dimensional structure of the complex which has been constructed from the reported atomic coordinates with the help of the PyMol molecular visualisation system. In the case of MAbs – carbohydrate crystalline complexes, a particular emphasis is given to indicate the conformation of the bound carbohydrate which can be viewed. The two three-dimensional structures can be displayed under Jmol applet windows that enable basic viewing and measurements options. The atomic coordinates at the PDB can be downloaded for further use.

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