Substructure and 3D pharmacophore searching involve the specification of a precise query, which is then used to search a database to identify compounds of interest. These approaches are clearly very useful ways to select compounds but they do have some limitations. First, one requires sufficient knowledge to be able to construct a meaningful substructure or 3D pharmacophore. However, this knowledge may not always be available if, for example, only one or two weakly active compounds are known. Second, in such searches a molecule either matches the query or it does not; as a consequence, the database is partitioned into two different sets with no sense of the relative ranking of the compounds. Finally, the user has no control over the size of the output. Thus, a query that is too general can result in an enormous number of hits whereas a very specific query may retrieve only a very small number of hits.
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© 2007 Springer
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(2007). Similarity Methods. In: An Introduction To Chemoinformatics. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-6291-9_5
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DOI: https://doi.org/10.1007/978-1-4020-6291-9_5
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