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    A New Method for Estimating the Importance of Hydrophobic Groups in the Binding Site of a Protein

    Access Status
    Fulltext not available
    Authors
    Kelly, M.
    Mancera, Ricardo
    Date
    2005
    Type
    Journal Article
    
    Metadata
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    Citation
    Kelly, M. and Mancera, R. 2005. A New Method for Estimating the Importance of Hydrophobic Groups in the Binding Site of a Protein. Journal of Medicinal Chemistry. 48: pp. 1069-1078.
    Source Title
    Journal of Medicinal Chemistry
    DOI
    10.1021/jm049524q
    ISSN
    00222623
    URI
    http://hdl.handle.net/20.500.11937/28078
    Collection
    • Curtin Research Publications
    Abstract

    Interactions between the hydrophobic regions of a binding site and those of a complementary ligand are often observed to provide the driving force for binding. We present a new method for the analysis of hydrophobic regions in the binding site of a protein that considers not only atom type but also the nonadditive effects arising from the shape and extent of a nonpolar region. The method has been parameterized using a purpose-built genetic algorithm to optimize its ability to identify those regions that are more likely to form a strong interaction with a non-polar ligand group. We demonstrate the ability of this method to account for changes in the shape and extent of the exposed nonpolar surface, using both artificial and protein examples. The method is also able to rationalize differences in binding affinity for ligand-protein complexes with largely hydrophobic binding sites.

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