Query features, representation

Although the representation of these queries is very similar to a combinatorial library, there are some significant differences in both design and use. Since the exact compositions of the database structures are not determined until after the query has been posed, the query typically contains query features, such as fuzzy atoms and bonds and ambiguous connectivity. There is no need for these features to represent a combinatorial library, since all the structures are known. The syntax for representing R-groups in a query can also include features such as zero occurrences to reduce the retrieval of undesired records. Such a feature is unnecessary for a combinatorial library representation, since it is a complete set of specific structures and not an open-ended query. 

The data representation underlying an interactively constructed query diagram may be, though seldom is, appropriate for direct use when scanning the database structures. The nature of the query determines the disposition of the underlying data. The vast majority of database searches are not simple identity checks, but substructural or similarity searches. The query features discovered by semantic analysis are applied as filters against the key indexes for the database. This results... 

Yak/Prgen and COMPASS work fundamentally with the surface of molecules, and derive representations of the predicted binding surface of the receptor ( pseudoreceptor ). APOLLO appears to work with features —groups on the molecule that meet specific topological criteria (i.e., which match a specified subgraph isomorphism query) these features must be defined by the user. 

A promising approach converts the structure information into a representation which is well suited to describing the IR spectral features. The transformation results in matrices containing information about a set of paths through the molecule. These matrices are combined, and a principal-component analysis finally leads to a rather short structure vector. This kind of description is derived for all structures in a database as well as for the query structure. The query structure is projected into the stmcture space, where it is a point surrounded by the point... 

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