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    Challenges and advances in computational docking: 2009 in review

    Access Status
    Fulltext not available
    Authors
    Yuriev, E.
    Agostino, Mark
    Ramsland, P.
    Date
    2011
    Type
    Journal Article
    
    Metadata
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    Citation
    Yuriev, E. and Agostino, M. and Ramsland, P. 2011. Challenges and advances in computational docking: 2009 in review. Journal of Molecular Recognition. 24 (2): pp. 149-164.
    Source Title
    Journal of Molecular Recognition
    DOI
    10.1002/jmr.1077
    ISSN
    1099-1352
    URI
    http://hdl.handle.net/20.500.11937/35703
    Collection
    • Curtin Research Publications
    Abstract

    Docking is a computational technique that places a small molecule (ligand) in the binding site of its macromolecular target (receptor) and estimates its binding affinity. This review addresses methodological developments that have occurred in the docking field in 2009, with a particular focus on the more difficult, and sometimes controversial, aspects of this promising computational discipline. These developments aim to address the main challenges of docking: receptor representation (such aspects as structural waters, side chain protonation, and, most of all, flexibility (from side chain rotation to domain movement)), ligand representation (protonation, tautomerism and stereoisomerism, and the effect of input conformation), as well as accounting for solvation and entropy of binding. This review is strongly focused on docking advances in the context of drug design, specifically in virtual screening and fragment-based drug design.

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