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    Molecular docking of carbohydrate ligands to antibodies: Structural validation against crystal structures

    Access Status
    Fulltext not available
    Authors
    Agostillo, M.
    Jene, C.
    Boyle, T.
    Ramsland, Paul
    Yuriev, E.
    Date
    2009
    Type
    Journal Article
    
    Metadata
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    Citation
    Agostillo, M. and Jene, C. and Boyle, T. and Ramsland, P. and Yuriev, E. 2009. Molecular docking of carbohydrate ligands to antibodies: Structural validation against crystal structures. Journal of Chemical Information and Modeling. 49 (12): pp. 2749-2760.
    Source Title
    Journal of Chemical Information and Modeling
    DOI
    10.1021/ci900388a
    ISSN
    1549-9596
    School
    School of Biomedical Sciences
    URI
    http://hdl.handle.net/20.500.11937/34925
    Collection
    • Curtin Research Publications
    Abstract

    Cell surface glycoproteins play vital roles in cellular homeostasis and disease. Antibody recognition of glycosylation on different cells and pathogens is critically important for immune surveillance. Conversely, adverse immune reactions resulting from antibody-carbohydrate interactions have been implicated in the development of autoimmune diseases and impact areas such as xenotransplantation and cancer treatment. Understanding the nature of antibody-carbohydrate interactions and the method by which saccharides fit into antibody binding sites is important in understanding the recognition process. In silico techniques offer attractive alternatives to experimental methods (X-ray crystallography and NMR) for the study of antibody-carbohydrate complexes. In particular, molecular docking provides information about protein-ligand interactions in systems that are difficult to study with experimental, techniques. Before molecular docking can be used to investigate antibody-carbohydrate complexes, validation of an appropriate docking method is required. In this study, four popular docking programs, Glide, AutoDock, GOLD, and FlexX, were assessed for their ability to accurately dock carbohydrates to antibodies. Comparison of top ranking poses with crystal structures highlighted the strengths and weaknesses of these programs. Rigid docking, in which the protein conformation remains static, and flexible docking, where both the protein and ligand are treated as flexible, were compared. This study has revealed that generally molecular docking of carbohydrates to antibodies has been performed best by Glide. © 2009 American Chemical Society.

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