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    Improvements, trends, and new ideas in molecular docking: 2012-2013 in review

    Access Status
    Fulltext not available
    Authors
    Yuriev, E.
    Holien, J.
    Ramsland, Paul
    Date
    2015
    Type
    Journal Article
    
    Metadata
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    Citation
    Yuriev, E. and Holien, J. and Ramsland, P. 2015. Improvements, trends, and new ideas in molecular docking: 2012-2013 in review. Journal of Molecular Recognition. 28 (10): pp. 581-604.
    Source Title
    Journal of Molecular Recognition
    DOI
    10.1002/jmr.2471
    ISSN
    0952-3499
    School
    School of Biomedical Sciences
    URI
    http://hdl.handle.net/20.500.11937/16780
    Collection
    • Curtin Research Publications
    Abstract

    Molecular docking is a computational method for predicting the placement of ligands in the binding sites of their receptor(s). In this review, we discuss the methodological developments that occurred in the docking field in 2012 and 2013, with a particular focus on the more difficult aspects of this computational discipline. The main challenges and therefore focal points for developments in docking, covered in this review, are receptor flexibility, solvation, scoring, and virtual screening. We specifically deal with such aspects of molecular docking and its applications as selection criteria for constructing receptor ensembles, target dependence of scoring functions, integration of higher-level theory into scoring, implicit and explicit handling of solvation in the binding process, and comparison and evaluation of docking and scoring methods.

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