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    Fragment-based Shape Signatures: A new tool for virtual screening and drug discovery

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    Fragment-based Shape Signatures ...
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    Genre
    Journal Article
    Date
    2013-12-01
    Author
    Zauhar, RJ
    Gianti, E
    Welsh, WJ
    Subject
    Ligand-based drug design
    Fragment-based shape signatures
    Scaffold hopping
    Shape signatures
    Shape similarity
    Virtual screening
    Permanent link to this record
    http://hdl.handle.net/20.500.12613/5356
    
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    DOI
    10.1007/s10822-013-9698-7
    Abstract
    Since its introduction in 2003, the Shape Signatures method has been successfully applied in a number of drug design projects. Because it uses a ray-tracing approach to directly measure molecular shape and properties (as opposed to relying on chemical structure), it excels at scaffold hopping, and is extraordinarily easy to use. Despite its advantages, a significant drawback of the method has hampered its application to certain classes of problems; namely, when the chemical structures considered are large and contain heterogeneous ring-systems, the method produces descriptors that tend to merely measure the overall size of the molecule, and begin to lose selective power. To remedy this, the approach has been reformulated to automatically decompose compounds into fragments using ring systems as anchors, and to likewise partition the ray-trace in accordance with the fragment assignments. Subsequently, descriptors are generated that are fragment-based, and query and target molecules are compared by mapping query fragments onto target fragments in all ways consistent with the underlying chemical connectivity. This has proven to greatly extend the selective power of the method, while maintaining the ease of use and scaffold-hopping capabilities that characterized the original implementation. In this work, we provide a full conceptual description of the next generation Shape Signatures, and we underline the advantages of the method by discussing its practical applications to ligand-based virtual screening. The new approach can also be applied in receptor-based mode, where protein-binding sites (partitioned into subsites) can be matched against the new fragment-based Shape Signatures descriptors of library compounds. © 2013 The Author(s).
    Citation to related work
    Springer Science and Business Media LLC
    Has part
    Journal of Computer-Aided Molecular Design
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    ae974a485f413a2113503eed53cd6c53
    http://dx.doi.org/10.34944/dspace/5338
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