Query features

Auto Build This application has been built upon the knowledge and experiences of our working group in order that beginner has access to all pertinent information. Auto Build automatically adds in the sample query structure the appropriate atom and bond query features. Then clicking on SSS button initiates a substructure search. Some examples of the query features, which may be added to a query structure, are ... 

M D Lmolfile Standardized file format for chemical structures including substructure query features (initially defined by Molecular Design Ltd)... 

The pharmacophore points in the Tripos implementation of DISCO, currently marketed under the name DISCOtech , can be represented as Tripos UNITY [56] query features and the models can be used directly for UNITY database searches or in combination with 3D QSAR such as CoMFA as described in [57]. 

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. 

Figure 9.13. Example 2D substructure search queries with various atom and bond query features. The more features that are present, the more flexible the search becomes, but the search may also require more time to complete. There is a trade-off between putting the flexibility into the database (i.e., storing and indexing multiple forms of a structure) and putting the flexibility into the search query and the search software.

Logic in Query Features. Using AND, OR, and NOT as modifiers on the application of query features. For example, one could run a search to select structures that contain "halogen and not primary or secondary amine, or not halogen and any amine." The logic can be a part of the query substructure, as with Markush queries, or it can be part of the SELECT statement. 

Another typical sitnation in the R D phase is that the scientist does not know enough about a structure to store this in a conventional structure database. In this case, generic structures can be used, which contain some placeholders (e.g., residues, superatoms, molecular masses, labels) on a part of the structure instead of the not yet known atoms or groups. An ELN in the research environment needs to provide means for storing this information and searching for it in combination with the known structure query features. 

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... 

Fuzzy 2D substructure searching is an extension of substructure searching to the minor extent that it permits the expansion of the query formulation vocabulary to include topological features and substructural wildcards described above. This involves the retrieval of all entities in a CIR system that contain the user-defined partial structure and that satisfy whatever wildcard specification pattern has been specified. The query identifies the partial structure and simple wildcard substitution patterns exactly. As with substructure searching, the use of query features on a partial structure will always identify structures which are equal in size or larger than the query. 

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